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Varela-Martínez E, Luigi-Sierra MG, Guan D, López-Béjar M, Casas E, Olvera-Maneu S, Gardela J, Palomo MJ, Osuagwuh UI, Ohaneje UL, Mármol-Sánchez E, Amills M. The landscape of long noncoding RNA expression in the goat brain. J Dairy Sci 2024; 107:4075-4091. [PMID: 38278299 DOI: 10.3168/jds.2023-23966] [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: 07/13/2023] [Accepted: 12/22/2023] [Indexed: 01/28/2024]
Abstract
The brain regulates multiple metabolic processes, such as food intake, energy expenditure, insulin secretion, hepatic glucose production, and glucose and fatty acid metabolism in adipose tissue, which are fundamental for the maintenance of energy and glucose homeostasis during lactation and pregnancy. In addition, brain expression has a fundamental impact on the development of maternal behavior. Although brain functions are partly regulated by long noncoding RNAs (lncRNAs), their expression profiles have not been characterized in depth in any ruminant species. We have sequenced the transcriptome of 12 brain tissues from 3 goats that were 1 mo pregnant and 4 nonpregnant goats to investigate their lncRNA expression patterns. Between 4,363 (adenohypophysis) and 4,604 (olfactory bulb) lncRNAs were expressed in brain tissues, leading us to establish a set of 794 already annotated lncRNAs and 5,098 novel lncRNA candidates. The detected lncRNAs shared features with those of other mammals, and tissue-specific lncRNAs were enriched in brain development-related terms. Differential expression analyses between goats that were 1 mo pregnant and nonpregnant goats showed that the lncRNA expression profiles of certain brain regions experience substantial changes associated with early pregnancy (238 lncRNAs are differentially expressed in the olfactory bulb), but others do not. Enrichment analysis showed that differentially expressed lncRNAs from the olfactory bulb are co-expressed with genes previously linked to behavioral changes related to pregnancy. These findings provide a first characterization of the landscape of lncRNA expression in the goat brain and provides valuable clues to understand the molecular events triggered by early pregnancy in the central nervous system.
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Affiliation(s)
- Endika Varela-Martínez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B. Sarriena, Leioa 48940, Spain; Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - María Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Manel López-Béjar
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Encarna Casas
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Sergi Olvera-Maneu
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Department of Veterinary Medicine, University of Nicosia School of Veterinary Medicine, 2414 Nicosia, Cyprus
| | - Jaume Gardela
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Maria Jesús Palomo
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Uchebuchi Ike Osuagwuh
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Uchechi Linda Ohaneje
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Department de Ciència Animal I dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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Ma X, Yang G, Zhang J, Ma R, Shen J, Feng F, Yu D, Huang C, Ma X, La Y, Wu X, Guo X, Chu M, Yan P, Liang C. Association between Single Nucleotide Polymorphisms of PRKD1 and KCNQ3 Gene and Milk Quality Traits in Gannan Yak ( Bos grunniens). Foods 2024; 13:781. [PMID: 38472894 DOI: 10.3390/foods13050781] [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: 01/12/2024] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Protein kinase D1 (PRKD1) functions primarily in normal mammary cells, and the potassium voltage-gated channel subfamily Q member 3 (KCNQ3) gene plays an important role in controlling membrane potential and neuronal excitability, it has been found that this particular gene is linked to the percentage of milk fat in dairy cows. The purpose of this study was to investigate the relationship between nucleotide polymorphisms (SNPs) of PRKD1 and KCNQ3 genes and the milk quality of Gannan yak and to find molecular marker sites that may be used for milk quality breeding of Gannan yak. Three new SNPs were detected in the PRKD1 (g.283,619T>C, g.283,659C>A) and KCNQ3 gene (g.133,741T>C) of 172 Gannan lactating female yaks by Illumina yak cGPS 7K liquid-phase microarray technology. Milk composition was analyzed using a MilkoScanTM milk composition analyzer. We found that the mutations of these three loci significantly improved the lactose, milk fat, casein, protein, non-fat milk solid (SNF) content and acidity of Gannan yaks. The lactose content of the TC heterozygous genotype population at g.283,619T>C locus was significantly higher than that of the TT wild-type population (p < 0.05); the milk fat content of the CA heterozygous genotype population at g.283,659C>A locus was significantly higher than that of the CC wild-type and AA mutant populations (p < 0.05); the casein, protein and acidity of the CC mutant and TC heterozygous groups at the g.133,741T>C locus were significantly higher than those of the wild type (p < 0.05), and the SNF of the TC heterozygous group was significantly higher than that of the mutant group (p < 0.05). The results showed that PRKD1 and KCNQ3 genes could be used as candidate genes affecting the milk traits of Gannan yak.
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Affiliation(s)
- Xiaoyong Ma
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Guowu Yang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Juanxiang Zhang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Rong Ma
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jinwei Shen
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Fen Feng
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Daoning Yu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Chun Huang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xiaoming Ma
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Yongfu La
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xiaoyun Wu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Ping Yan
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Institute of Western Agriculture, The Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Chunnian Liang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
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Yang G, Zhang J, Ma X, Ma R, Shen J, Liu M, Yu D, Feng F, Huang C, Ma X, La Y, Guo X, Yan P, Liang C. Polymorphisms of CCSER1 Gene and Their Correlation with Milk Quality Traits in Gannan Yak ( Bos grunniens). Foods 2023; 12:4318. [PMID: 38231770 DOI: 10.3390/foods12234318] [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: 10/22/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 01/19/2024] Open
Abstract
Coiled-coil serine-rich protein 1 (CCSER 1) gene is a regulatory protein gene. This gene has been reported to be associated with various economic traits in large mammals in recent years. The aim of this study was to investigate the association between CCSER1 gene single nucleotide polymorphisms (SNPs) and Gannan yaks and to identify potential molecular marker loci for breeding milk quality in Gannan yaks. We genotyped 172 Gannan yaks using Illumina Yak cGPS 7K liquid microarrays and analyzed the correlation between the three SNPs loci of the CCSER1 gene and the milk qualities of Gannan yaks, including milk fat, protein and casein. It was found that mutations at the g.183,843A>G, g.222,717C>G and g.388,723G>T loci all affected the fat, protein, casein and lactose traits of Gannan yak milk to varying extents, and that the milk quality of individuals with mutant phenotypes was significantly improved. Among them, the milk fat content of AG heterozygous genotype population at g.183,843A>G locus was significantly higher than that of AA and GG genotype populations (p < 0.05); the casein and protein content of mutant GG and CG genotype populations at g.222,717C>G locus was significantly higher than that of wild-type CC genotype population (p < 0.05); and the g.388,723G>T locus of the casein and protein contents of the mutant TT genotype population were significantly higher (p < 0.05) than those of the wild-type GG genotype population. These results provide potential molecular marker sites for Gannan yak breeding.
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Affiliation(s)
- Guowu Yang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- College of Life Sciences and Engineering, Northwest Minzu University, Lanzhou 730106, China
| | - Juanxiang Zhang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xiaoyong Ma
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Rong Ma
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jinwei Shen
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Modian Liu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Daoning Yu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- College of Life Sciences and Engineering, Northwest Minzu University, Lanzhou 730106, China
| | - Fen Feng
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Chun Huang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xiaoming Ma
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Yongfu La
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Ping Yan
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Chunnian Liang
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
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Xia W, Liu Y, Loor JJ, Bionaz M, Jiang M. Dynamic Profile of the Yak Mammary Transcriptome during the Lactation Cycle. Animals (Basel) 2023; 13:ani13101710. [PMID: 37238139 DOI: 10.3390/ani13101710] [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: 02/16/2023] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
The objective of this study was to assess the transcriptome of the mammary tissue of four yaks during the whole lactation cycle. For this purpose, biopsies of the mammary gland were performed at -30, -15, 1, 15, 30, 60, 120, 180, and 240 days relative to parturition (d). The transcriptome analysis was performed using a commercial bovine microarray platform and the results were analyzed using several bioinformatic tools. The statistical analysis using an overall false discovery rate ≤ 0.05 for the effect of whole lactation and p < 0.05 for each comparison identified >6000 differentially expressed genes (DEGs) throughout lactation, with a large number of DEGs observed at the onset (1 d vs. -15 d) and at the end of lactation (240 d vs. 180 d). Bioinformatics analysis revealed a major role of genes associated with BTA3, BTA4, BTA6, BTA9, BTA14, and BTA28 in lactation. Functional analysis of DEG underlined an overall induction of lipid metabolism, suggesting an increase in triglycerides synthesis, likely regulated by PPAR signaling. The same analysis revealed an induction of amino acid metabolism and secretion of protein, with a concomitant decrease in proteasome, indicating a major role of amino acid handling and reduced protein degradation in the synthesis and secretion of milk proteins. Glycan biosynthesis was induced for both N-glycan and O-glycan, suggesting increased glycan content in the milk. The cell cycle and immune response, especially antigen processing and presentation, were strongly inhibited during lactation, suggesting that morphological changes are minimized during lactation, while the mammary gland prevents immune hyper-response. Transcripts associated with response to radiation and low oxygen were enriched in the down-regulated DEG affected by the stage of lactation. Except for this last finding, the functions affected by the transcriptomic adaptation to lactation in mammary tissue of yak are very similar to those observed in dairy cows.
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Affiliation(s)
- Wei Xia
- College of Animal and Veterinary Science, Southwest Minzu University, Chengdu 610041, China
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Yili Liu
- College of Animal and Veterinary Science, Southwest Minzu University, Chengdu 610041, China
| | - Juan J Loor
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Massimo Bionaz
- Department of Animal and Rangeland Sciences, Oregon State University, 112 Withycombe Hall, Corvallis, OR 97331, USA
| | - Mingfeng Jiang
- College of Animal and Veterinary Science, Southwest Minzu University, Chengdu 610041, China
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Xuan R, Zhao X, Li Q, Zhao Y, Wang Y, Du S, Duan Q, Guo Y, Ji Z, Chao T, Wang J. Characterization of long noncoding RNA in nonlactating goat mammary glands reveals their regulatory role in mammary cell involution and remodeling. Int J Biol Macromol 2022; 222:2158-2175. [DOI: 10.1016/j.ijbiomac.2022.09.291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022]
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Wu X, Ayalew W, Chu M, Pei J, Liang C, Bao P, Guo X, Yan P. Characterization of RNA Editome in the Mammary Gland of Yaks during the Lactation and Dry Periods. Animals (Basel) 2022; 12:ani12020207. [PMID: 35049829 PMCID: PMC8773173 DOI: 10.3390/ani12020207] [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: 11/17/2021] [Revised: 01/01/2022] [Accepted: 01/14/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary In order to study the influence of RNA editing sites on lactation and mammary gland development process in yaks, we comprehensively characterized the RNA editome of the yak mammary gland during the lactation period and dry period by using the transcriptome and genome sequencing data. The results revealed 82,872 nonredundant RNA editing sites, 14,159 of which were differentially edited between the lactation period and dry period. Enrichment analysis showed that the genes harboring differential editing sites were mainly associated with mammary gland development-related pathways, such as MAPK pathway, PI3K-Akt pathway, FoxO signaling pathway, GnRH signaling pathway, and focal adhesion pathway. Our findings offer some novel insights into the RNA editing function in the mammary gland of yaks. Abstract The mammary gland is a complicated organ comprising several types of cells, and it undergoes extensive morphogenetic and metabolic changes during the female reproductive cycle. RNA editing is a posttranscriptional modification event occurring at the RNA nucleotide level, and it drives transcriptomic and proteomic diversities, with potential functional consequences. RNA editing in the mammary gland of yaks, however, remains poorly understood. Here, we used REDItools to identify RNA editing sites in mammary gland tissues in yaks during the lactation period (LP, n = 2) and dry period (DP, n = 3). Totally, 82,872 unique RNA editing sites were identified, most of which were detected in the noncoding regions with a low editing degree. In the coding regions (CDS), we detected 5235 editing sites, among which 1884 caused nonsynonymous amino acid changes. Of these RNA editing sites, 486 were found to generate novel possible miRNA target sites or interfere with the initial miRNA binding sites, indicating that RNA editing was related to gene regulation mediated by miRNA. A total of 14,159 RNA editing sites (involving 3238 common genes) showed a significant differential editing level in the LP when compared with that in the DP through Tukey’s Honest Significant Difference method (p < 0.05). According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, genes that showed different RNA editing levels mainly participated in pathways highly related to mammary gland development, including MAPK, PI3K-Akt, FoxO, and GnRH signaling pathways. Collectively, this work demonstrated for the first time the dynamic RNA editome profiles in the mammary gland of yaks and shed more light on the mechanism that regulates lactation together with mammary gland development.
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Affiliation(s)
- Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
| | - Wondossen Ayalew
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
- Department of Animal Production and Technology, Wolkite University, Wolkite P.O. Box 07, Ethiopia
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
- Correspondence: (X.G.); (P.Y.)
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.W.); (W.A.); (M.C.); (J.P.); (C.L.); (P.B.)
- Correspondence: (X.G.); (P.Y.)
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Chen Z, Wang J, Ma J, Li S, Huo S, Yang Y, Zhaxi Y, Zhao Y, Zhang D. Transcriptome and proteome analysis of pregnancy and postpartum anoestrus ovaries in yak. J Vet Sci 2022. [DOI: 10.4142/jvs.2022.23.e3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Zhou Chen
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Jine Wang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Junyuan Ma
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Shuyuan Li
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Shengdong Huo
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Yanmei Yang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Yingpai Zhaxi
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Yongqing Zhao
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Derong Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
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Chen Z, Wang J, Ma J, Li S, Huo S, Yang Y, Zhaxi Y, Zhao Y, Zhang D. Transcriptome and proteome analysis of pregnancy and postpartum anoestrus ovaries in yak. J Vet Sci 2022; 23:e3. [PMID: 35088950 PMCID: PMC8799938 DOI: 10.4142/jvs.21195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/10/2021] [Accepted: 09/25/2021] [Indexed: 11/20/2022] Open
Affiliation(s)
- Zhou Chen
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Jine Wang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Junyuan Ma
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Shuyuan Li
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Shengdong Huo
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Yanmei Yang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Yingpai Zhaxi
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Yongqing Zhao
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Derong Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730030, China
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Qiao H, Wang J, Wang Y, Yang J, Wei B, Li M, Wang B, Li X, Cao Y, Tian L, Li D, Yao L, Kan Y. Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori. BMC Genomics 2021; 22:374. [PMID: 34022797 PMCID: PMC8140452 DOI: 10.1186/s12864-021-07692-1] [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: 02/09/2021] [Accepted: 05/06/2021] [Indexed: 12/13/2022] Open
Abstract
Background 20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is induced by 20E in the larval fat body. Long non-coding RNAs (lncRNAs) function in various biological processes in many organisms, including insects. Many lncRNAs have been reported to be potential for autophagy occurrence in mammals, but it has not been investigated in insects. Results RNA libraries from the fat body of B. mori dissected at 2 and 6 h post-injection with 20E were constructed and sequenced, and comprehensive analysis of lncRNAs and mRNAs was performed. A total of 1035 lncRNAs were identified, including 905 lincRNAs and 130 antisense lncRNAs. Compared with mRNAs, lncRNAs had longer transcript length and fewer exons. 132 lncRNAs were found differentially expressed at 2 h post injection, compared with 64 lncRNAs at 6 h post injection. Thirty differentially expressed lncRNAs were common at 2 and 6 h post-injection, and were hypothesized to be associated with the 20E response. Target gene analysis predicted 6493 lncRNA-mRNA cis pairs and 42,797 lncRNA-mRNA trans pairs. The expression profiles of LNC_000560 were highly consistent with its potential target genes, Atg4B, and RNAi of LNC_000560 significantly decreased the expression of LNC_000560 and Atg4B. These results indicated that LNC_000560 was potentially involved in the 20E-induced autophagy of the fat body by regulating Atg4B. Conclusions This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B. mori. LNC_000560 and its potential target gene were identified to be related to 20-regulated autophagy in B. mori. These results will be helpful for further studying the regulatory mechanisms of lncRNAs in autophagy and other biological processes in this insect model. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07692-1.
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Affiliation(s)
- Huili Qiao
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Jingya Wang
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China.,School of Life Science, Zhengzhou University, 450001, Zhengzhou, Henan, China
| | - Yuanzhuo Wang
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Juanjuan Yang
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Bofan Wei
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Miaomiao Li
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China.,School of Life Science, Zhengzhou University, 450001, Zhengzhou, Henan, China
| | - Bo Wang
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Xiaozhe Li
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Yang Cao
- State Key Laboratory of Silkworm Genome Biology / Biological Science Research Center, Southwest University, 400716, Chongqing, China.,Guangdong Laboratory for Lingnan Modern Agriculture/Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Ling Tian
- Guangdong Laboratory for Lingnan Modern Agriculture/Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642, Guangzhou, Guangdong, China
| | - Dandan Li
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Lunguang Yao
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China
| | - Yunchao Kan
- China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, 473061, Nanyang, Henan, China.
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