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Qin X, He X, Chen L, Han Y, Yun Y, Wu J, Sha L, Borjigin G. Transcriptome analysis of adipose tissue in grazing cattle: Identifying key regulators of fat metabolism. Open Life Sci 2024; 19:20220843. [PMID: 38681730 PMCID: PMC11049749 DOI: 10.1515/biol-2022-0843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/05/2024] [Accepted: 02/20/2024] [Indexed: 05/01/2024] Open
Abstract
The taste and tenderness of meat are the main determinants of carcass quality in many countries. This study aimed to discuss the mechanisms of intramuscular fat deposition in grazing and house-breeding cattle. We performed transcriptome analysis to characterize messenger RNA and microRNA (miRNA) expression profiles. A total of 456 and 66 differentially expressed genes (DEGs) and differentially expressed (DE) miRNAs were identified in the adipose tissue of grazing and house-breeding cattle. Kyoto Encyclopedia of Genes and Genomes pathway analysis identified the association of DEGs with fatty acid metabolism, fatty acid degradation, peroxisome proliferator-activated receptors signaling pathway, adenosine monophosphate-activated protein kinase signaling pathway, adipocytokine signaling pathway, and the association of DE miRNAs with mitogen-activated protein kinase signaling pathway. Apolipoprotein L domain containing 1, pyruvate dehydrogenase kinase 4, and sphingosine-1-phosphate lyase 1 genes may be the key regulators of fat metabolism in grazing cattle. Finally, we found that miR-211 and miR-331-5p were negatively correlated with the elongation of very long-chain fatty acids protein 6 (ELOVL6), and miR-331-5p might be the new regulator involved in fat metabolism. The results indicated that ELOVL6 participated in various functions and pathways related to fat metabolism. Meanwhile, miR-331-5p, as a new regulator, might play an essential role in this process. Our findings laid a more in-depth and systematic research foundation for the formation mechanism and characteristics of adipose tissue in grazing cattle.
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Affiliation(s)
- Xia Qin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
- Pharmacy and Materials School, Huainan Union University, Huainan232038, China
| | - Xige He
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Lu Chen
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Yunfei Han
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Yueying Yun
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Jindi Wu
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Lina Sha
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
| | - Gerelt Borjigin
- College of Food Science and Engineering, Inner Mongolia Agricultural University, #306 Zhaowuda Road, Saihan District, Huhhot, Inner Mongolia 010018, China
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MacPhillamy C, Ren Y, Chen T, Hiendleder S, Low WY. MicroRNA breed and parent-of-origin effects provide insights into biological pathways differentiating cattle subspecies in fetal liver. Front Genet 2023; 14:1329939. [PMID: 38162682 PMCID: PMC10757722 DOI: 10.3389/fgene.2023.1329939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction: MicroRNAs (miRNAs) play a crucial role in regulating gene expression during key developmental processes, including fetal development. Brahman (Bos taurus indicus) and Angus (Bos taurus taurus) cattle breeds represent two major cattle subspecies with strikingly different phenotypes. Methods: We analyzed miRNA expression in liver samples of purebred and reciprocal crosses of Angus and Brahman to investigate breed and parent-of-origin effects at the onset of accelerated fetal growth. Results: We identified eight novel miRNAs in fetal liver samples and 14 differentially expressed miRNAs (DEMs) between purebred samples. Correlation of gene expression modules and miRNAs by breed and parent-of-origin effects revealed an enrichment of genes associated with breed-specific differences in traits such as heat tolerance (Brahman) and fat deposition (Angus). We demonstrate that genes predicted to be targets of DEMs were more likely to be differentially expressed than non-targets (p-value < 0.05). We identified several miRNAs (bta-miR-187, bta-miR-216b, bta-miR-2284c, bta-miR-2285c, bta-miR-2285cp, bta-miR-2419-3p, bta-miR-2419-5p, and bta-miR-11984) that showed similar correlation patterns as bta-miR-2355-3p, which has been associated with the glutamatergic synapse pathway, a key facilitator of heat tolerance. Furthermore, we report Angus-breed-specific miRNAs (bta-miR-2313-5p, btamiR-490, bta-miR-2316, and bta-miR-11990) that may be involved in fat deposition. Finally, we showed that the DEMs identified in fetal liver are involved in Rap1, MAPK, and Ras signalling pathways, which are important for fetal development, muscle development and metabolic traits such as fat metabolism. Conclusion: Our work sheds light on the miRNA expression patterns that contribute to gene expression differences driving phenotypic differences in indicine and taurine cattle.
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Affiliation(s)
- Callum MacPhillamy
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Tong Chen
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Stefan Hiendleder
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
- Robinson Research Institute, The University of Adelaide, North Adelaide, SA, Australia
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
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Long F, Wang X, Wan Y, Zhang Z, Zhang W, Zan L, Cheng G. Bta-miR-493 Inhibits Bovine Preadipocytes Differentiation by Targeting BMPR1A via the TGFβ/BMP and p38MAPK Signaling Pathways. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14641-14653. [PMID: 36373418 DOI: 10.1021/acs.jafc.2c05719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fat deposition significantly impacts the meat yield and the meat quality of beef cattle, which is closely associated with the preadipocyte proliferation and differentiation. Bta-miR-493 is expressed differentially in the backfat of Qinchuan cattle of various ages, and it may be involved in the fat accumulation of beef cattle. However, the role and functional mechanism of bta-miR-493 in fat deposition are still unclear. Tissue-specific expression analysis showed that the level of bta-miR-493 was moderately abundant in the adipose tissues of beef cattle. Moreover, the expression of bta-miR-493 in perirenal fat, subcutaneous fat, and longissimus dorsi muscle of Japanese black cattle was significantly higher than that in Qinchuan cattle. EdU staining, cell counting assay, and Oil Red O staining indicated that bta-miR-493 promoted the proliferation of bovine preadipocytes but inhibited their differentiation. The dual luciferase assay and transcriptomic analysis confirmed that bone morphogenetic protein receptor 1A (BMPR1A) is a target gene of bta-miR-493. Moreover, rescue experiments showed that bta-miR-493 could promote bovine preadipocyte proliferation but inhibit their differentiation by targeting BMPR1A via the TGFβ/BMP and p38MAPK signaling pathways. Overall, our findings revealed a bta-miR-493-BMPR1A-TGFβ/BMP/p38MAPK regulatory axis that will serve as a theoretical foundation for the molecular breeding of beef cattle with high intramuscular fat deposition.
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Affiliation(s)
- Feng Long
- College of Animal Science and Technology, Northwest A&F University, Yangling712100, Shaanxi, China
| | - Xiaoyu Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling712100, Shaanxi, China
| | - Yuan Wan
- College of Animal Science and Technology, Northwest A&F University, Yangling712100, Shaanxi, China
| | - Ziyi Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling712100, Shaanxi, China
| | - Wenzhen Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling712100, Shaanxi, China
| | - Linsen Zan
- National Beef Cattle Improvement Centre, College of Animal Science and Technology, Northwest A&F University, Yangling712100, Shaanxi, China
| | - Gong Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling712100, Shaanxi, China
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Zhang S, Jiang E, Kang Z, Bi Y, Liu H, Xu H, Wang Z, Lei C, Chen H, Lan X. CircRNA Profiling Reveals an Abundant circBDP1 that Regulates Bovine Fat Development by Sponging miR-181b/miR-204 Targeting Sirt1/TRARG1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14312-14328. [PMID: 36269615 DOI: 10.1021/acs.jafc.2c05939] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The proliferation and differentiation of preadipocytes is an important factor determining bovine fat development, which is closely related to the feed conversion ratio, carcass traits, and beef quality. The purpose of this study was to identify the effects of candidate circRNA and miRNA on the proliferation and differentiation of bovine preadipocytes in order to provide basic materials for molecular breeding in cattle. circRNA sequencing was performed on bovine adipocyte samples at different differentiation time points, and a total of 1830 differentially expressed circRNAs were identified. Among them, circBDP1, derived from the bovine BDP1 gene, has potential binding sites for miR-204 (known as a regulator of bovine fat development) and miR-181b, which gives us a hint that circBDP1 may regulate bovine fat development by adsorbing miR-204 and miR-181b. Here, our results revealed that circBDP1 overexpression promoted the proliferation and differentiation of bovine preadipocytes. The miRNA profile of bovine adipocytes at different differentiation time points was also analyzed using the small RNA sequencing method, and a total of 89 differentially expressed miRNAs were identified, including miR-204 and miR-181b. As expected, dual-luciferase reporter results showed that circBDP1 competitively adsorbed miR-181b and miR-204. Overexpression and interference of miR-181b in bovine preadipocytes and 3T3-L1 showed that miR-181b promoted the proliferation and differentiation of preadipocytes. Further results displayed that miR-181b and miR-204 simultaneously targeted the SIRT1 gene, and miR-204 also targeted the 3' UTR region of the TRARG1 gene. In summary, this study found that miR-181b and miR-204 were involved in fat development by targeting SIRT1 and TRARG1. The results of this study will lay a foundation for the research of fat development and beef cattle industry.
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Affiliation(s)
- Sihuan Zhang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei230036, P.R. China
| | - Enhui Jiang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
| | - Zihong Kang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100193, China
| | - Yi Bi
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
| | - Hongfei Liu
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing100193, China
| | - Han Xu
- School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong510006, China
| | - Zhen Wang
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing100193, China
| | - Chuzhao Lei
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
| | - Hong Chen
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
| | - Xianyong Lan
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi712100, China
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Li Y, Yang M, Lou A, Yun J, Ren C, Li X, Xia G, Nam K, Yoon D, Jin H, Seo K, Jin X. Integrated analysis of expression profiles with meat quality traits in cattle. Sci Rep 2022; 12:5926. [PMID: 35396568 PMCID: PMC8993808 DOI: 10.1038/s41598-022-09998-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 03/31/2022] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) play a vital role in improving meat quality by binding to messenger RNAs (mRNAs). We performed an integrated analysis of miRNA and mRNA expression profiling between bulls and steers based on the differences in meat quality traits. Fat and fatty acids are the major phenotypic indices of meat quality traits to estimate between-group variance. In the present study, 90 differentially expressed mRNAs (DEGs) and 18 differentially expressed miRNAs (DEMs) were identified. Eighty-three potential DEG targets and 18 DEMs were used to structure a negative interaction network, and 75 matching target genes were shown in this network. Twenty-six target genes were designated as intersection genes, screened from 18 DEMs, and overlapped with the DEGs. Seventeen of these genes enriched to 19 terms involved in lipid metabolism. Subsequently, 13 DEGs and nine DEMs were validated using quantitative real-time PCR, and seven critical genes were selected to explore the influence of fat and fatty acids through hub genes and predict functional association. A dual-luciferase reporter and Western blot assays confirmed a predicted miRNA target (bta-miR-409a and PLIN5). These findings provide substantial evidence for molecular genetic controls and interaction among genes in cattle.
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Affiliation(s)
- Yunxiao Li
- College of Life Science, Shandong University, Qingdao, China
| | - Miaosen Yang
- Department of Chemistry, Northeast Electric Power University, Jilin, China
| | - Angang Lou
- Department of Veterinary Medicine, College of Agriculture, Yanbian University, Yanji, China
| | - Jinyan Yun
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Jilin, China
| | - Chunyu Ren
- Animal Husbandry Bureau of Yanbian Autonomous Prefecture, Yanji, China
| | - Xiangchun Li
- Department of Veterinary Medicine, College of Agriculture, Yanbian University, Yanji, China
| | - Guangjun Xia
- Department of Veterinary Medicine, College of Agriculture, Yanbian University, Yanji, China
| | - Kichang Nam
- Department of Animal Science and Technology, College of Life Science and Natural Resources, Sunchon National University, Sunchon, South Korea
| | - Duhak Yoon
- Department of Animal Science, Kyungpook National University, Taegu, South Korea
| | - Haiguo Jin
- Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Kangseok Seo
- Department of Animal Science and Technology, College of Life Science and Natural Resources, Sunchon National University, Sunchon, South Korea.
| | - Xin Jin
- Engineering Research Center of North-East Cold Region Beef Cattle Science and Technology Innovation, Ministry of Education, Yanbian University, Yanji, China.
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6
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Pieri M, Theori E, Dweep H, Flourentzou M, Kalampalika F, Maniori MA, Papagregoriou G, Papaneophytou C, Felekkis K. A bovine miRNA, bta-miR-154c, withstands in vitro human digestion but does not affect cell viability of colorectal human cell lines after transfection. FEBS Open Bio 2022; 12:925-936. [PMID: 35318810 PMCID: PMC9063428 DOI: 10.1002/2211-5463.13402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/02/2022] [Accepted: 03/21/2022] [Indexed: 11/05/2022] Open
Abstract
Colorectal cancer (CRC) is the third most frequent human cancer with over 1.3 million new cases globally. CRC is a complex disease caused by interactions between genetic and environmental factors; in particular, high consumption of red meat, including beef, is considered a risk factor for CRC initiation and progression. Recent data demonstrate that exogenous microRNAs (miRNAs) entering the body via ingestion could pose an effect on the consumer. In this study, we focused on bovine miRNAs that do not share a seed sequence with humans and mice. We identified bta-miR-154c, a bovine miRNA found in edible parts of beef and predicted via cross-species bioinformatic analysis to affect cancer-related pathways in human cells. When bovine tissue was subjected to cooking and a simulation of human digestion, bta-miR-154c was still detected after all procedures, albeit at reduced concentrations. However, lipofection of bta-miR-154c in three different colorectal human cell lines did not affect their viability as evaluated at various time points and concentrations. These data indicate that bta-miR-154c (a) may affect cancer-related pathways in human cells, (b) can withstand digestion and be detected after all stages of an in vitro digestion protocol, but (c) it does not appear to alter epithelial cell viability after entering human enterocytes, even at supraphysiological amounts. Further experiments will elucidate whether bta-miR-154c exerts a different functional effect on the human gut epithelium, which may cause it to contribute to CRC progression through its consumption.
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Affiliation(s)
- Myrtani Pieri
- Department of Life and Health Sciences, University of Nicosia, Cyprus
| | - Elena Theori
- Department of Life and Health Sciences, University of Nicosia, Cyprus
| | - Harsh Dweep
- The Wistar Institute, Philadelphia, Pennsylvania, USA
| | | | | | | | | | | | - Kyriacos Felekkis
- Department of Life and Health Sciences, University of Nicosia, Cyprus
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Taylor RK, McCarty KM, LeMaster CT, Ricks RE, Pratt SL, Long NM. Effects of nutrient restriction during early or mid-gestation in bovine on placental development and miRNA expression in the cotyledon. Anim Reprod Sci 2022; 237:106935. [PMID: 35093729 DOI: 10.1016/j.anireprosci.2022.106935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 01/07/2022] [Accepted: 01/23/2022] [Indexed: 11/23/2022]
Abstract
The objective of this study was to determine effects of maternal nutrient restriction (NR) during early or mid-gestation on uterine composition and miRNA expression in cotyledons. Primiparous Angus-cross cows (n = 38) were synchronized and inseminated using male sexed semen, blocked by body condition score and body weight (BW), and assigned to treatments. Animals were fed either: control (CON; gain 1 kg/week) or NR (55% maintenance energy and crude protein requirements) based on BW. An initial set of animals were fed either NR (n = 8) or CON (n = 8) from day 30-110 of gestation. A second set of animals were fed CON (n = 8) d 30-190 (CON/CON); NR (n = 7) day 30-110 followed by CON day 110-190 (NR/CON); or CON (n = 7) day 30-110 followed by NR day 110-190 (CON/NR). Cows were harvested on day 110 or 190 of gestation to collect placental tissues. RNA was isolated from cotyledon samples (3 animals/group) prior to microarray analysis using known Bos taurus microRNA sequences. Relative microRNA abundance was analyzed via ANOVA. Maternal NR increased (P < 0.05) cotyledon weight and total placentome surface area irrespective of gestational day. At day 110 of gestation, 51 microRNAs were reduced while 91 microRNAs observed greater abundance (P < 0.05) in NR verses CON cotyledons. At day 190 of gestation, 40 microRNAs were reduced and 26 microRNAs were increased (P < 0.05) in both NR/CON and CON/NR verses CON cotyledons. Top KEGG pathway analysis included: axon guidance, endocytosis, neuroactive ligand receptor interaction, and MAPK signaling pathway. Early-gestation maternal NR altered microRNA abundance to a greater extent than mid-gestation NR.
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Affiliation(s)
- R K Taylor
- Department of Animal and Veterinary Sciences, Clemson University, Clemson, SC 29634, USA
| | - K M McCarty
- Department of Animal and Veterinary Sciences, Clemson University, Clemson, SC 29634, USA
| | - C T LeMaster
- Department of Animal and Veterinary Sciences, Clemson University, Clemson, SC 29634, USA
| | - R E Ricks
- Department of Animal and Veterinary Sciences, Clemson University, Clemson, SC 29634, USA
| | - S L Pratt
- Department of Animal and Veterinary Sciences, Clemson University, Clemson, SC 29634, USA
| | - N M Long
- Department of Animal and Veterinary Sciences, Clemson University, Clemson, SC 29634, USA.
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Zhang J, Long K, Wang J, Zhang J, Jin L, Tang Q, Li X, Ma J, Li M, Jiang A. Yak miR-2285o-3p attenuates hypoxia-induced apoptosis by targeting caspase-3. Anim Genet 2021; 53:49-57. [PMID: 34807998 PMCID: PMC9298924 DOI: 10.1111/age.13153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 12/01/2022]
Abstract
miRNAs are a class of hairpin‐derived RNAs, 21–24 nucleotides in length, which are involved in a range of biological processes. The bta‐miR‐2285 family has over 40 members spanning the entire bovine genome. We previously found that bta‐miR‐2285o‐3p was highly expressed in yak heart and lung when compared with cattle, which prompted us to investigate its potential function in high‐altitude adaptation of yaks. In this study, we detected wide‐spread high expression of bta‐miR‐2285o‐3p in yak tissues. Further experiments revealed that the protein tyrosine phosphatase receptor type M (PTPRM) gene was the host gene of bta‐miR‐2285o‐3p and that two linked SNPs in bta‐mir‐2285o precursor affected the biogenesis of mature miRNA (bta‐miR‐2285o‐3p). Functional analysis in vitro indicated that bta‐miR‐2285o‐3p attenuated hypoxia‐induced apoptosis by targeting very low‐density lipoprotein receptor (VLDLR), phosphatase and tensin homolog (PTEN) and caspase‐3. Expression level analysis in vivo revealed the high negative Pearson’s correlation between bta‐miR‐2285o‐3p and caspase3 in yak, highlighting the potential important roles of bta‐miR‐2285o‐3p in yak high‐altitude adaptation. Our study provides a typical model for deciphering the function of miRNAs in environmental adaptation.
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Affiliation(s)
- J Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - K Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - J Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - J Zhang
- Chongqing Academy of Animal Science, Rongchang, Chongqing, 402460, China
| | - L Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Q Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - X Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - J Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - M Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - A Jiang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
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Wang L, Zhang S, Cheng G, Mei C, Li S, Zhang W, Junjvlieke Z, Zan L. MiR-145 reduces the activity of PI3K/Akt and MAPK signaling pathways and inhibits adipogenesis in bovine preadipocytes. Genomics 2020; 112:2688-2694. [DOI: 10.1016/j.ygeno.2020.02.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/31/2020] [Accepted: 02/29/2020] [Indexed: 12/29/2022]
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10
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Wang L, Zhang S, Zhang W, Cheng G, Khan R, Junjvlieke Z, Li S, Zan L. miR-424 Promotes Bovine Adipogenesis Through an Unconventional Post-Transcriptional Regulation of STK11. Front Genet 2020; 11:145. [PMID: 32194625 PMCID: PMC7064614 DOI: 10.3389/fgene.2020.00145] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/07/2020] [Indexed: 11/26/2022] Open
Abstract
Adipose tissue is the largest energy reservoir and secretory organ in the animal body, and is essential for maintaining normal physiological functions and metabolic balance. MicroRNAs regulate the process of adipogenic differentiation through post-transcriptional regulatory mechanisms. In the present study, miR-424 was upregulated during bovine adipocyte differentiation both in vivo and in vitro. The overexpression and interference of miR-424 exhibited the positive regulatory role in the differentiation of bovine adipocytes. Furthermore, miR-424 directly binds to the three prime untranslated region (3' UTR) of serine/threonine kinase 11 (STK11, also called LKB1), a master upstream gene in the AMP-activated protein kinase (AMPK) cascade, and up-regulates its expression. Functional studies showed that the knockdown of STK11 attenuated the pro-adipogenic effect of miR-424. Post-transcriptional regulation of STK11 by miR-424 was mediated potentially in an RNA binding protein (RBP) binding site-dependent manner. In conclusion, our study shows that miR-424 promotes bovine adipogenesis through an unconventional post-transcriptional regulation of STK11, which may serve as a potential target for the regulation of bovine adipogenesis and the improvement of livestock breeding efficiency.
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Affiliation(s)
- Li Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Song Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wenzhen Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zainaguli Junjvlieke
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shijun Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,National Beef Cattle Improvement Center, Northwest A&F University, Yangling, China
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Silva-Vignato B, Coutinho LL, Cesar ASM, Poleti MD, Regitano LCA, Balieiro JCC. Comparative muscle transcriptome associated with carcass traits of Nellore cattle. BMC Genomics 2017; 18:506. [PMID: 28673252 PMCID: PMC5496360 DOI: 10.1186/s12864-017-3897-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/22/2017] [Indexed: 01/16/2023] Open
Abstract
Background Commercial cuts yield is an important trait for beef production, which affects the final value of the products, but its direct determination is a challenging procedure to be implemented in practice. The measurement of ribeye area (REA) and backfat thickness (BFT) can be used as indirect measures of meat yield. REA and BFT are important traits studied in beef cattle due to their strong implication in technological (carcass yield) and nutritional characteristics of meat products, like the degree of muscularity and total body fat. Thus, the aim of this work was to study the Longissimus dorsi muscle transcriptome of Nellore cattle, associated with REA and BFT, to find differentially expressed (DE) genes, metabolic pathways, and biological processes that may regulate these traits. Results By comparing the gene expression level between groups with extreme genomic estimated breeding values (GEBV), 101 DE genes for REA and 18 for BFT (false discovery rate, FDR 10%) were identified. Functional enrichment analysis for REA identified two KEGG pathways, MAPK (Mitogen-Activated Protein Kinase) signaling pathway and endocytosis pathway, and three biological processes, response to endoplasmic reticulum stress, cellular protein modification process, and macromolecule modification. The MAPK pathway is responsible for fundamental cellular processes, such as growth, differentiation, and hypertrophy. For BFT, 18 biological processes were found to be altered and grouped into 8 clusters of semantically similar terms. The DE genes identified in the biological processes for BFT were ACHE, SRD5A1, RSAD2 and RSPO3. RSAD2 has been previously shown to be associated with lipid droplet content and lipid biosynthesis. Conclusion In this study, we identified genes, metabolic pathways, and biological processes, involved in differentiation, proliferation, protein turnover, hypertrophy, as well as adipogenesis and lipid biosynthesis related to REA and BFT. These results enlighten some of the molecular processes involved in muscle and fat deposition, which are economically important carcass traits for beef production. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3897-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bárbara Silva-Vignato
- College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635-900, Brazil.
| | - Luiz L Coutinho
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Aline S M Cesar
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Mirele D Poleti
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Júlio C C Balieiro
- College of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, SP, 13635-900, Brazil
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Wei Y, Cui YF, Tong HL, Zhang WW, Yan YQ. MicroRNA-2400 promotes bovine preadipocyte proliferation. Biochem Biophys Res Commun 2016; 478:1054-9. [PMID: 27514450 DOI: 10.1016/j.bbrc.2016.08.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 08/06/2016] [Indexed: 11/27/2022]
Abstract
MicroRNAs (miRNAs) play critical roles in the proliferation of bovine preadipocytes. miR-2400 is a novel and unique miRNA from bovines. In the present study, we separated and identified preadipocytes from bovine samples. miR-2400 overexpression increased the rate of preadipocyte proliferation, which was analyzed with a combination of EdU and flow cytometry. Simultaneously, functional genes related to proliferation (PCNA, CCND2, CCNB1) were also increased, which was detected by real-time PCR. Furthermore, luciferase reporter assays showed that miR-2400 bound directly to the 3'untranslated regions (3'UTRs) of PRDM11 mRNA. These data suggested that miR-2400 could promote preadipocyte proliferation by targeting PRDM11.
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Affiliation(s)
- Yao Wei
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Ya Feng Cui
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Hui Li Tong
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Wei Wei Zhang
- College of Life Sciences and Agriculture & Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Yun Qin Yan
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
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Lee S, Hwang S, Yu HJ, Oh D, Choi YJ, Kim MC, Kim Y, Ryu DY. Expression of microRNAs in Horse Plasma and Their Characteristic Nucleotide Composition. PLoS One 2016; 11:e0146374. [PMID: 26731407 PMCID: PMC4711666 DOI: 10.1371/journal.pone.0146374] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 12/16/2015] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) in blood plasma are stable under high levels of ribonuclease activity and could function in tissue-to-tissue communication, suggesting that they may have distinctive structural characteristics compared with non-circulating miRNAs. In this study, the expression of miRNAs in horse plasma and their characteristic nucleotide composition were examined and compared with non-plasma miRNAs. Highly expressed plasma miRNA species were not part of the abundant group of miRNAs in non-plasma tissues, except for the eca-let-7 family. eca-miR-486-5p, -92a, and -21 were among the most abundant plasma miRNAs, and their human orthologs also belong to the most abundant group of miRNAs in human plasma. Uracil and guanine were the most common nucleotides of both plasma and non-plasma miRNAs. Cytosine was the least common in plasma and non-plasma miRNAs, although levels were higher in plasma miRNAs. Plasma miRNAs also showed higher expression levels of miRNAs containing adenine and cytosine repeats, compared with non-plasma miRNAs. These observations indicate that miRNAs in the plasma have a unique nucleotide composition.
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Affiliation(s)
- Seungwoo Lee
- BK21 Plus Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Seungwoo Hwang
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Hee Jeong Yu
- BK21 Plus Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Dayoung Oh
- BK21 Plus Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Yu Jung Choi
- BK21 Plus Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Myung-Chul Kim
- BK21 Plus Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Yongbaek Kim
- BK21 Plus Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Doug-Young Ryu
- BK21 Plus Program for Creative Veterinary Science Research, Research Institute for Veterinary Science and College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
- * E-mail:
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Genome-wide analysis of microRNAs identifies the lipid metabolism pathway to be a defining factor in adipose tissue from different sheep. Sci Rep 2015; 5:18470. [PMID: 26690086 PMCID: PMC4686875 DOI: 10.1038/srep18470] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/17/2015] [Indexed: 02/05/2023] Open
Abstract
MicroRNAs are short (17–24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. In recent years, deep sequencing of the transcriptome is increasingly being utilized with the promise of higher sensitivity for the identification of differential expression patterns as well as the opportunity to discover new transcripts, including new alternative isoforms and miRNAs. Here, we utilized RNA-seq technology to perform a genome-wide analysis of miRNAs from the adipose tissue of the two species of sheep to look for clues that might explain the fat deposition differences between the sheep. The RNA-seq analysis detected 3132 miRNAs from the adipose tissue of the Small-tail Han and Dorset sheep, of which 2893 were defined as potential new miRNAs. In addition, 54 miRNAs were differentially expressed between the two breeds of sheep. Gene ontology and pathway analyses of the predicted target genes that negatively associated with the differentially expressed miRNAs revealed that there was less active lipid metabolism in the adipose tissue of Small Tail Han sheep. This study can help understand the underling mechanisms responsible for the morphological differences related to fat deposition between two breeds of sheep.
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Mahmoudi A, Zargaran A, Amini HR, Assadi A, Vajdi Hokmabad R, Eghbalsaied S. A SNP in the 3′-untranslated region of AMPKγ1 may associate with serum ketone body and milk production of Holstein dairy cows. Gene 2015; 574:48-52. [DOI: 10.1016/j.gene.2015.07.077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 07/23/2015] [Indexed: 12/21/2022]
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Ibeagha-Awemu EM, Zhao X. Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs. Front Genet 2015; 6:302. [PMID: 26442116 PMCID: PMC4585011 DOI: 10.3389/fgene.2015.00302] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 09/11/2015] [Indexed: 12/30/2022] Open
Abstract
Improvement in animal productivity has been achieved over the years through careful breeding and selection programs. Today, variations in the genome are gaining increasing importance in livestock improvement strategies. Genomic information alone, however, explains only a part of the phenotypic variance in traits. It is likely that a portion of the unaccounted variance is embedded in the epigenome. The epigenome encompasses epigenetic marks such as DNA methylation, histone tail modifications, chromatin remodeling, and other molecules that can transmit epigenetic information such as non-coding RNA species. Epigenetic factors respond to external or internal environmental cues such as nutrition, pathogens, and climate, and have the ability to change gene expression leading to emergence of specific phenotypes. Accumulating evidence shows that epigenetic marks influence gene expression and phenotypic outcome in livestock species. This review examines available evidence of the influence of epigenetic marks on livestock (cattle, sheep, goat, and pig) traits and discusses the potential for consideration of epigenetic markers in livestock improvement programs. However, epigenetic research activities on farm animal species are currently limited partly due to lack of recognition, funding and a global network of researchers. Therefore, considerable less attention has been given to epigenetic research in livestock species in comparison to extensive work in humans and model organisms. Elucidating therefore the epigenetic determinants of animal diseases and complex traits may represent one of the principal challenges to use epigenetic markers for further improvement of animal productivity.
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Affiliation(s)
- Eveline M. Ibeagha-Awemu
- Dairy and Swine Research and Development Centre, Agriculture and Agri-Food CanadaSherbrooke, QC, Canada
| | - Xin Zhao
- Department of Animal Science, McGill University, Ste-Anne-De-BellevueQC, Canada
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