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Li C, Zhu J, Shi H, Luo J, Zhao W, Shi H, Xu H, Wang H, Loor JJ. Comprehensive Transcriptome Profiling of Dairy Goat Mammary Gland Identifies Genes and Networks Crucial for Lactation and Fatty Acid Metabolism. Front Genet 2020; 11:878. [PMID: 33101357 PMCID: PMC7545057 DOI: 10.3389/fgene.2020.00878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/17/2020] [Indexed: 11/17/2022] Open
Abstract
Milk fatty acids secreted by the mammary gland are one of the most important determinants of the nutritional value of goat milk. Unlike cow milk, limited data are available on the transcriptome-wide changes across stages of lactation in dairy goats. In this study, goat mammary gland tissue collected at peak lactation, cessation of milking, and involution were analyzed with digital gene expression (DGE) sequencing to generate longitudinal transcript profiles. A total of 51,299 unigenes were identified and further annotated to 12,763 genes, of which 9,131 were differentially expressed across various stages of lactation. Most abundant genes and differentially expressed genes (DEGs) were functionally classified through clusters of euKaryotic Orthologous Groups (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A total of 16 possible expression patterns were uncovered, and 13 genes were deemed novel candidates for regulation of lactation in the goat: POLG, SPTA1, KLC, GIT2, COPS3, PDP, CD31, USP16/29/37, TLL1, NCAPH, ABI2, DNAJC4, and MAPK8IP3. In addition, PLA2, CPT1, PLD, GGA, SRPRB, and AP4S1 are proposed as novel and promising candidates regulating mammary fatty acid metabolism. “Butirosin and neomycin biosynthesis” and “Glyoxylate and dicarboxylate metabolism” were the most impacted pathways, and revealed novel metabolic alterations in lipid metabolism as lactation progressed. Overall, the present study provides new insights into the synthesis and metabolism of fatty acids and lipid species in the mammary gland along with more detailed information on molecular regulation of lactogenesis. The major findings will benefit efforts to further improve milk quality in dairy goats.
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Affiliation(s)
- Cong Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Jiangjiang Zhu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Hengbo Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China.,College of Animal Science, Zhejiang University, Hangzhou, China
| | - Jun Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Wangsheng Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Huaiping Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Huifen Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Hui Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, China
| | - Juan J Loor
- Mammalian NutriPhysioGenomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL, United States
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Discovery of genes and proteins possibly regulating mean wool fibre diameter using cDNA microarray and proteomic approaches. Sci Rep 2020; 10:7726. [PMID: 32382132 PMCID: PMC7206055 DOI: 10.1038/s41598-020-64903-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/30/2020] [Indexed: 01/06/2023] Open
Abstract
Wool fibre diameter (WFD) is one of the wool traits with higher economic impact. However, the main genes specifically regulating WFD remain unidentified. In this current work we have used Agilent Sheep Gene Expression Microarray and proteomic technology to investigate the gene expression patterns of body side skin, bearing more wool, in Aohan fine wool sheep, a Chinese indigenous breed, and compared them with that of small tail Han sheep, a sheep bread with coarse wool. Microarray analyses showed that most of the genes likely determining wool diameter could be classified into a few categories, including immune response, regulation of receptor binding and growth factor activity. Certain gene families might play a role in hair growth regulation. These include growth factors, immune cytokines, solute carrier families, cellular respiration and glucose transport amongst others. Proteomic analyses also identified scores of differentially expressed proteins.
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Zhang Y, Zhang S, Guan W, Chen F, Cheng L, Lv Y, Chen J. GLUT1 and lactose synthetase are critical genes for lactose synthesis in lactating sows. Nutr Metab (Lond) 2018; 15:40. [PMID: 29946342 PMCID: PMC6001073 DOI: 10.1186/s12986-018-0276-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/07/2018] [Indexed: 11/10/2022] Open
Abstract
Background Lactose synthesis rate is an important factor in milk production and quality in mammals. Understanding the lactose synthesis mechanism is crucial for the improvement of milk quantity and quality. However, research on the temporal gene changes regarding lactose synthesis during the whole lactation is still limited. The objective of this study was to determine gene expression profiles related to lactose synthesis in sows during lactation, and further identify the critical steps or key factors in the lactose synthesis pathway. Methods To determine the temporal change of factors related to lactose synthesis in sows, milk from eight multiparous Yorkshire sows (parity 3 to 6) was collected at 0 h, 2 h, 6 h, 12 h, 24 h, day 2, 3, 4, 7, 14, and 21 after birth of the first piglet. Lactose content, prolactin and progesterone concentration, and gene or protein expression related to lactose synthesis were measured. Results The lactose yield increased gradually from D2 to D21 and reached a maximum at D14 (3-fold from D2) during lactation (P < 0.05). A similar trend was observed in IGF-1 and insulin concentrations in milk, both of which were greatest at D3 with a subsequent decrease during middle to late lactation. Conversely, milk prolactin and progesterone concentrations moderately decreased with the progression of lactation. The mRNA or protein expressions related to glucose transportation (GLUT1), glucose-galactose interconversion (HK1 and UGP2), UDP-galactose transportation (SLC35A2), and lactose synthetase (LALBA and B4GALT1) in the lactose synthesis pathway were significantly upregulated during early to middle lactation and plateaued by late lactation (P < 0.05). Conclusions These novel findings suggest that the increased lactose synthesis in lactation was related to the coordinated upregulation of genes or enzymes in the lactose synthesis pathway, and glucose transportation (GLUT1) and lactose synthetase (LALBA and B4GALT1) might be the critical steps in the lactose synthesis pathway of sows during lactation.
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Affiliation(s)
- Yinzhi Zhang
- 1Guangdong Province Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Shihai Zhang
- 1Guangdong Province Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Wutai Guan
- 1Guangdong Province Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China.,2College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Wushan Avenue, Tianhe District, Guangzhou, 510642 China
| | - Fang Chen
- 1Guangdong Province Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Lin Cheng
- 1Guangdong Province Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yantao Lv
- 1Guangdong Province Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jun Chen
- 1Guangdong Province Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, China
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Muhaghegh-Dolatabady M, Rahimi Rezaei A. Sequence Characterization in 3′-Flanking Region of Bovine TNF-α: Association with Milk Production Traits and Somatic Cell Score in Holstein Cattle of Iran. IRANIAN JOURNAL OF BIOTECHNOLOGY 2018. [DOI: 10.21859/ijb.1195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Lee HK, Willi M, Wang C, Yang CM, Smith HE, Liu C, Hennighausen L. Functional assessment of CTCF sites at cytokine-sensing mammary enhancers using CRISPR/Cas9 gene editing in mice. Nucleic Acids Res 2017; 45:4606-4618. [PMID: 28334928 PMCID: PMC5416830 DOI: 10.1093/nar/gkx185] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/15/2017] [Indexed: 01/05/2023] Open
Abstract
The zinc finger protein CTCF has been invoked in establishing boundaries between genes, thereby controlling spatial and temporal enhancer activities. However, there is limited genetic evidence to support the concept that these boundaries restrict the search space of enhancers. We have addressed this question in the casein locus containing five mammary and two non-mammary genes under the control of at least seven putative enhancers. We have identified two CTCF binding sites flanking the locus and two associated with a super-enhancer. Individual deletion of these sites from the mouse genome did not alter expression of any of the genes. However, deletion of the border CTCF site separating the Csn1s1 mammary enhancer from neighboring genes resulted in the activation of Sult1d1 at a distance of more than 95 kb but not the more proximal and silent Sult1e1 gene. Loss of this CTCF site led to de novo interactions between the Sult1d1 promoter and several enhancers in the casein locus. Our study demonstrates that only one out of the four CTCF sites in the casein locus had a measurable in vivo activity. Studies on additional loci are needed to determine the biological role of CTCF sites associated with enhancers.
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Affiliation(s)
- Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA.,Department of Cell and Developmental Biology & Dental Research Institute, Seoul National University, Seoul 110-749, Korea
| | - Michaela Willi
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA.,Division of Bioinformatics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Chaochen Wang
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Chul Min Yang
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Harold E Smith
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Chengyu Liu
- Transgenic Core,National Heart Lung and Blood Institute, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive and Kidney Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
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Crisà A, Ferrè F, Chillemi G, Moioli B. RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk. BMC Vet Res 2016; 12:264. [PMID: 27884183 PMCID: PMC5123407 DOI: 10.1186/s12917-016-0881-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/07/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND In this work we aimed at sequencing and assembling the goat milk transcriptome corresponding at colostrum and 120 days of lactation. To reconstruct transcripts we used both the genome as reference, and a de novo assembly approach. Additionally, we aimed at identifying the differentially expressed genes (DEGs) between the two lactation stages and at analyzing the expression of genes involved in oligosaccharides metabolism. RESULTS A total of 44,635 different transcripts, organized in 33,757 tentative genes, were obtained using the goat genome as reference. A significant sequence similarity match was found for 40,353 transcripts (90%) against the NCBI NT and for 35,701 (80%) against the NR databases. 68% and 69% of the de novo assembled transcripts, in colostrum and 120 days of lactation samples respectively, have a significant match with the merged transcriptome obtained using Cufflinks/Cuffmerge. CSN2, PAEP, CSN1S2, CSN3, LALBA, TPT1, FTH1, M-SAA3, SPP1, GLYCAM1, EEF1A1, CTSD, FASN, RPS29, CSN1S1, KRT19 and CHEK1 were found between the top fifteen highly expressed genes. 418 loci were differentially expressed between lactation stages, among which 207 and 122 were significantly up- and down-regulated in colostrum, respectively. Functional annotation and pathway enrichment analysis showed that in goat colostrum somatic cells predominate biological processes involved in glycolysis, carbohydrate metabolism, defense response, cytokine activity, regulation of cell proliferation and cell death, vasculature development, while in mature milk, biological process associated with positive regulation of lymphocyte activation and anatomical structure morphogenesis are enriched. The analysis of 144 different oligosaccharide metabolism-related genes showed that most of these (64%) were more expressed in colostrum than in mature milk, with eight expressed at very high levels (SLCA3, GMSD, NME2, SLC2A1, B4GALT1, B3GNT2, NANS, HEXB). CONCLUSIONS To our knowledge, this is the first study comparing goat transcriptome of two lactation stages: colostrum and 120 days. Our findings suggest putative differences of expression between stages and can be envisioned as a base for further research in the topic. Moreover because a higher expression of genes involved in immune defense response, carbohydrate metabolism and related to oligosaccharide metabolism was identified in colostrum we here corroborate the potential of goat milk as a natural source of lactose-derived oligosaccharides and for the development of functional foods.
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Affiliation(s)
- Alessandra Crisà
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Animal production research centre, Via Salaria 31, 00015, Monterotondo, Rome, Italy.
| | - Fabrizio Ferrè
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, Via Belmeloro 6, 40126, Bologna, Italy
| | - Giovanni Chillemi
- Applications and Innovation Department, CINECA, SCAI SuperComputing, Via dei Tizii 6, 00185, Rome, Italy
| | - Bianca Moioli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Animal production research centre, Via Salaria 31, 00015, Monterotondo, Rome, Italy
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Transcriptome-Wide Analysis Reveals the Role of PPAR γ Controlling the Lipid Metabolism in Goat Mammary Epithelial Cells. PPAR Res 2016; 2016:9195680. [PMID: 27818678 PMCID: PMC5081438 DOI: 10.1155/2016/9195680] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 07/13/2016] [Accepted: 07/25/2016] [Indexed: 11/17/2022] Open
Abstract
To explore the large-scale effect of peroxisome proliferator-activated receptor γ (PPARG) in goat mammary epithelial cells (GMEC), an oligonucleotide microarray platform was used for transcriptome profiling in cells overexpressing PPARG and incubated with or without rosiglitazone (ROSI, a PPARγ agonist). A total of 1143 differentially expressed genes (DEG) due to treatment were detected. The Dynamic Impact Approach (DIA) analysis uncovered the most impacted and induced pathways “fatty acid elongation in mitochondria,” “glycosaminoglycan biosynthesis-keratan sulfate,” and “pentose phosphate pathway.” The data highlights the central role of PPARG in milk fatty acid metabolism via controlling fatty acid elongation, biosynthesis of unsaturated fatty acid, lipid formation, and lipid secretion; furthermore, its role related to carbohydrate metabolism promotes the production of intermediates required for milk fat synthesis. Analysis of upstream regulators indicated that PPARG participates in multiple physiological processes via controlling or cross talking with other key transcription factors such as PPARD and NR1H3 (also known as liver-X-receptor-α). This transcriptome-wide analysis represents the first attempt to better understand the biological relevance of PPARG expression in ruminant mammary cells. Overall, the data underscored the importance of PPARG in mammary lipid metabolism and transcription factor control.
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Zhao J, Liu N, Liu K, He J, Yu J, Bu R, Cheng M, De W, Liu J, Li H. Identification of genes and proteins associated with anagen wool growth. Anim Genet 2016; 48:67-79. [PMID: 27611105 DOI: 10.1111/age.12480] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2016] [Indexed: 02/03/2023]
Abstract
Identifying genes of major effect for wool growth would offer strategies for improving the quality and increasing the yield of fine wool. In this study, we employed the Agilent Sheep Gene Expression Microarray and proteomic technology to investigate the gene expression patterns of body side skin (more wool growing) in Aohan fine wool sheep (a Chinese indigenous breed) in comparison with groin skin (no wool growing) at the anagen stage of the wool follicle. A microarray study revealed that 4772 probes were differentially expressed, including 2071 upregulated and 2701 downregulated probes, in the comparisons of body side skin vs. groin skin (S/G). The microarray results were verified by means of quantitative PCR. A total of 1099 probes were assigned to unique genes/transcripts. The number of distinct genes/transcripts (annotated) was 926, of which 352 were upregulated and 574 were downregulated. In S/G, 13 genes were upregulated by more than 10 fold, whereas 60 genes were downregulated by more than 10 fold. Further analysis revealed that the majority of the genes possibly related to the wool growth could be assigned to categories including regulation of cell division, intermediate filament, cytoskeletal part and growth factor activity. Several potential gene families may participate in hair growth regulation, including fibroblast growth factors, transforming growth factor-β, WNTs, insulin-like growth factor, vascular endothelial growth factors and so on. Proteomic analysis also revealed 196 differentially expressed protein points, of which 121 were identified as single protein points.
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Affiliation(s)
- J Zhao
- Qingdao Agricultural University, Qingdao, 266109, China.,Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China.,China Agricultural University, Beijing, 100193, China
| | - N Liu
- Qingdao Agricultural University, Qingdao, 266109, China
| | - K Liu
- Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China
| | - J He
- Qingdao Agricultural University, Qingdao, 266109, China
| | - J Yu
- Qingdao Agricultural University, Qingdao, 266109, China
| | - R Bu
- Qingdao Agricultural University, Qingdao, 266109, China
| | - M Cheng
- Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China
| | - W De
- Nanjing Medical University, Nanjing, 210029, China
| | - J Liu
- Qingdao Agricultural University, Qingdao, 266109, China
| | - H Li
- Qingdao Agricultural University, Qingdao, 266109, China.,Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China
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Osorio JS, Lohakare J, Bionaz M. Biosynthesis of milk fat, protein, and lactose: roles of transcriptional and posttranscriptional regulation. Physiol Genomics 2016; 48:231-56. [DOI: 10.1152/physiolgenomics.00016.2015] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The demand for high-quality milk is increasing worldwide. The efficiency of milk synthesis can be improved by taking advantage of the accumulated knowledge of the transcriptional and posttranscriptional regulation of genes coding for proteins involved in the synthesis of fat, protein, and lactose in the mammary gland. Research in this area is relatively new, but data accumulated in the last 10 years provide a relatively clear picture. Milk fat synthesis appears to be regulated, at least in bovines, by an interactive network between SREBP1, PPARγ, and LXRα, with a potential role for other transcription factors, such as Spot14, ChREBP, and Sp1. Milk protein synthesis is highly regulated by insulin, amino acids, and amino acid transporters via transcriptional and posttranscriptional routes, with the insulin-mTOR pathway playing a central role. The transcriptional regulation of lactose synthesis is still poorly understood, but it is clear that glucose transporters play an important role. They can also cooperatively interact with amino acid transporters and the mTOR pathway. Recent data indicate the possibility of nutrigenomic interventions to increase milk fat synthesis by feeding long-chain fatty acids and milk protein synthesis by feeding amino acids. We propose a transcriptional network model to account for all available findings. This model encompasses a complex network of proteins that control milk synthesis with a cross talk between milk fat, protein, and lactose regulation, with mTOR functioning as a central hub.
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Affiliation(s)
| | - Jayant Lohakare
- Oregon State University, Corvallis, Oregon; and
- Kangwon National University, Chuncheon, South Korea
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Bentley PA, Wall EH, Dahl GE, McFadden TB. Responses of the mammary transcriptome of dairy cows to altered photoperiod during late gestation. Physiol Genomics 2015; 47:488-99. [PMID: 26175502 DOI: 10.1152/physiolgenomics.00112.2014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 07/13/2015] [Indexed: 11/22/2022] Open
Abstract
Cows exposed to short day photoperiod (SD, 8L:16D) during the 60-day nonlactating period prior to parturition produce more milk in their subsequent lactation compared with cows exposed to long day photoperiod (LD, 16L:8D). Although this response is well established in dairy cows, the underlying mechanisms are not understood. We hypothesized that differential gene expression in cows exposed to SD or LD photoperiods during the dry period could be used to identify the functional basis for the subsequent increase in milk production during lactation. Pregnant, multiparous cows were maintained on an SD or LD photoperiod for 60 days prior to parturition. Mammary biopsies were obtained on days -24 and -9 relative to parturition and Affymetrix GeneChip Bovine Genome Arrays were used to quantify gene expression. Sixty-four genes were differentially expressed (P ≤ 0.05 and fold-change ≥ |1.5|) between SD and LD treatments. Many of these genes were associated with cell growth and proliferation, or immune function. Ingenuity Pathway Analysis predicted upstream regulators to include TNF, TGF-β1, interferon-γ, and several interleukins. In addition, expression of 125 genes was significantly different between day -24 and day -9; those genes were associated with milk component metabolism and immune function. The interaction of photoperiod and time affected 32 genes associated with insulin-like growth factor I signaling. Genes differentially expressed in response to photoperiod were associated with mammary development and immune function consistent with the enhancement of milk yield in the ensuing lactation. Our results provide insight into the mechanisms by which photoperiod affects the mammary gland and subsequently lactation.
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Affiliation(s)
- P A Bentley
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - E H Wall
- Department of Animal Science, University of Vermont, Burlington, Vermont
| | - G E Dahl
- Department of Animal Sciences, University of Florida, Gainesville, Florida; and
| | - T B McFadden
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada; Department of Animal Science, University of Vermont, Burlington, Vermont; Division of Animal Sciences, University of Missouri, Columbia, Missouri
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Liu N, Li H, Liu K, Yu J, Bu R, Cheng M, De W, Liu J, He G, Zhao J. Identification of skin-expressed genes possibly associated with wool growth regulation of Aohan fine wool sheep. BMC Genet 2014; 15:144. [PMID: 25511509 PMCID: PMC4272822 DOI: 10.1186/s12863-014-0144-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 12/03/2014] [Indexed: 11/25/2022] Open
Abstract
Background Sheep are valuable resources for the animal fibre industry. Therefore, identifying genes which regulate wool growth would offer strategies for improving the quality of fine wool. In this study, we employed Agilent sheep gene expression microarray and proteomic technology to compare the gene expression patterns of the body side (hair-rich) and groin (hairless) skins of Aohan fine wool sheep (a Chinese indigenous breed). Results Comparing the body side to the groin skins (S/G) of Aohan fine wool sheep, the microarray study revealed that 1494 probes were differentially expressed, including 602 more highly expressed and 892 less highly expressed probes. The microarray results were verified by means of quantitative PCR. Cluster analysis could distinguish the body side skin and the groin skin. Based on the Database for Annotation, Visualization and Integrated Discovery (DAVID), 38 of the differentially expressed genes were classified into four categories, namely regulation of receptor binding, multicellular organismal process, protein binding and macromolecular complex. Proteomic study revealed that 187 protein spots showed significant (p < 0.05) differences in their respective expression levels. Among them, 46 protein entries were further identified by MALDI-TOF/MS analyses. Conclusions Microarray analysis revealed thousands of differentially expressed genes, many of which were possibly associated with wool growth. Several potential gene families might participate in hair growth regulation. Proteomic analysis also indentified hundreds of differentially expressed proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0144-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nan Liu
- Qingdao Agricultural University, Qingdao, 266109, China.
| | - Hegang Li
- Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China.
| | - Kaidong Liu
- Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China.
| | - Juanjuan Yu
- Qingdao Agricultural University, Qingdao, 266109, China.
| | - Ran Bu
- Qingdao Agricultural University, Qingdao, 266109, China.
| | - Ming Cheng
- Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China.
| | - Wei De
- Nanjing Medical University, Nanjing, 210002, China.
| | - Jifeng Liu
- Qingdao Agricultural University, Qingdao, 266109, China.
| | - Guangling He
- State key Laboratory of Hydroscience and Engineering, Beijing, 100084, China.
| | - Jinshan Zhao
- Qingdao Agricultural University, Qingdao, 266109, China. .,Qingdao Institute of Animal Science and Veterinary Medicine, Qingdao, 266100, China. .,China Agricultural University, Beijing, 100193, China.
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12
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Zhao WS, Hu SL, Yu K, Wang H, Wang W, Loor J, Luo J. Lipoprotein lipase, tissue expression and effects on genes related to fatty acid synthesis in goat mammary epithelial cells. Int J Mol Sci 2014; 15:22757-71. [PMID: 25501331 PMCID: PMC4284735 DOI: 10.3390/ijms151222757] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 11/11/2014] [Accepted: 11/24/2014] [Indexed: 01/08/2023] Open
Abstract
Lipoprotein lipase (LPL) serves as a central factor in hydrolysis of triacylglycerol and uptake of free fatty acids from the plasma. However, there are limited data concerning the action of LPL on the regulation of milk fat synthesis in goat mammary gland. In this investigation, we describe the cloning and sequencing of the LPL gene from Xinong Saanen dairy goat mammary gland, along with a study of its phylogenetic relationships. Sequence analysis showed that goat LPL shares similarities with other species including sheep, bovine, human and mouse. LPL mRNA expression in various tissues determined by RT-qPCR revealed the highest expression in white adipose tissue, with lower expression in heart, lung, spleen, rumen, small intestine, mammary gland, and kidney. Expression was almost undetectable in liver and muscle. The expression profiles of LPL gene in mammary gland at early, peak, mid, late lactation, and the dry period were also measured. Compared with the dry period, LPL mRNA expression was markedly greater at early lactation. However, compared with early lactation, the expression was lower at peak lactation and mid lactation. Despite those differences, LPL mRNA expression was still greater at peak, mid, and late lactation compared with the dry period. Using goat mammary epithelial cells (GMEC), the in vitro knockdown of LPL via shRNA or with Orlistat resulted in a similar degree of down-regulation of LPL (respectively). Furthermore, knockdown of LPL was associated with reduced mRNA expression of SREBF1, FASN, LIPE and PPARG but greater expression of FFAR3. There was no effect on ACACA expression. Orlistat decreased expression of LIPE, FASN, ACACA, and PPARG, and increased FFAR3 and SREBF1 expression. The pattern of LPL expression was similar to the changes in milk fat percentage in lactating goats. Taken together, results suggest that LPL may play a crucial role in fatty acid synthesis.
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Affiliation(s)
- Wang-Sheng Zhao
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Shi-Liang Hu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Kang Yu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Hui Wang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Wei Wang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Juan Loor
- Mammalian NutriPhysioGenomics, Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois, Urbana, IL 61801, USA.
| | - Jun Luo
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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13
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Genes regulating lipid and protein metabolism are highly expressed in mammary gland of lactating dairy goats. Funct Integr Genomics 2014; 15:309-21. [PMID: 25433708 DOI: 10.1007/s10142-014-0420-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 11/17/2014] [Accepted: 11/20/2014] [Indexed: 10/24/2022]
Abstract
Dairy goats serve as an important source of milk and also fulfill agricultural and economic roles in developing countries. Understanding the genetic background of goat mammary gland is important for research on the regulatory mechanisms controlling tissue function and the synthesis of milk components. We collected tissue at four different stages of goat mammary gland development and generated approximately 25 GB of data from Illumina de novo RNA sequencing. The combined reads were assembled into 51,361 unigenes, and approximately 60.07 % of the unigenes had homology to other proteins in the NCBI non-redundant protein database (NR). Functional classification through eukaryotic Ortholog Groups of Protein (KOG), gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that the unigenes from goat mammary glands are involved in a wide range of biological processes and metabolic pathways, including lipid metabolism and lactose metabolism. The results of qPCR revealed that genes encoding FABP3, FASN, SCD, PLIN2, whey proteins (LALBA and BLG), and caseins (CSN1S1, CSN1S2, CSN2 and CSN3) at 100 and 310 days postpartum increased significantly compared with the non-lactating period. In addition to their role in lipid and protein synthesis, the higher expression at 310 days postpartum could contribute to mammary cell turnover during pregnancy. In conclusion, this is the first study to characterize the complete transcriptome of goat mammary glands and constitutes a comprehensive genomic resource available for further studies of ruminant lactation.
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14
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Yudin NS, Aitnazarov RB, Voevoda MI, Gerlinskaya LA, Moshkin MP. Association of polymorphism harbored by tumor necrosis factor alpha gene and sex of calf with lactation performance in cattle. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:1379-87. [PMID: 25049721 PMCID: PMC4093077 DOI: 10.5713/ajas.2013.13114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 05/22/2013] [Accepted: 05/14/2013] [Indexed: 01/24/2023]
Abstract
In a majority of mammals, male infants have heavier body mass and grow faster than female infants. Accordingly, male offspring nursing requires a much greater maternal energy contribution to lactation. It is possible that the maternal-fetal immunoendocrine dialog plays an important role in female preparation for lactation during pregnancy. Immune system genes are an integral part of gene regulatory networks in lactation and tumor necrosis factor alpha (TNFα) is a proinflammatory cytokine that also plays an important role in normal mammary gland development. The aim of this study was to evaluate the influence of the sex of calf and/or the -824A/G polymorphism in the promoter region of TNFα gene on milk performance traits in Black Pied cattle over the course of lactation. We also studied the allele frequency differences of -824A/G variants across several cattle breeds, which were bred in different climatic conditions. The G allele frequency decreased gradually over the course of lactation events in the Black Pied dairy cattle because of a higher culling rate of cows with the G/G genotype (p<0.001). In contrast to the genotypes A/A and A/G, cows with G/G genotype showed significant variability of milk and milk fat yield subject to sex of delivered calf. Milk yield and milk fat yield were significantly higher in the case of birth of a bull calf than with a heifer calf (p<0.03). The G allele frequency varies from 48% to 58% in Grey Ukrainian and Black Pied cattle to 77% in aboriginal Yakut cattle. Our results suggest that the TNFα -824A/G gene polymorphism may have an influence on the reproductive efforts of cows over the course of lactation events depending on the sex of progeny. Allocation of resources according to sex of the calf allows optimizing the energy cost of lactation. This may be a probable reason for high G allele frequency in Yakut cattle breeding in extreme environmental conditions. Similarly, the dramatic fall in milk production after birth of a heifer calf increases the probability of culling for the cows with the G/G genotype in animal husbandry.
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Affiliation(s)
- N S Yudin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences,Novosibirsk 630090, Russian Federation
| | - R B Aitnazarov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences,Novosibirsk 630090, Russian Federation
| | - M I Voevoda
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences,Novosibirsk 630090, Russian Federation
| | - L A Gerlinskaya
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences,Novosibirsk 630090, Russian Federation
| | - M P Moshkin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences,Novosibirsk 630090, Russian Federation
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15
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Liu N, Li H, Liu K, Yu J, Cheng M, De W, Liu J, Shi S, He Y, Zhao J. Differential expression of genes and proteins associated with wool follicle cycling. Mol Biol Rep 2014; 41:5343-9. [PMID: 24847760 DOI: 10.1007/s11033-014-3405-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/06/2014] [Indexed: 01/31/2023]
Abstract
Sheep are valuable resources for the wool industry. Wool growth of Aohan fine wool sheep has cycled during different seasons in 1 year. Therefore, identifying genes that control wool growth cycling might lead to ways for improving the quality and yield of fine wool. In this study, we employed Agilent sheep gene expression microarray and proteomic technology to compare the gene expression patterns of the body side skins at August and December time points in Aohan fine wool sheep (a Chinese indigenous breed). Microarray study revealed that 2,223 transcripts were differentially expressed, including 1,162 up-regulated and 1,061 down-regulated transcripts, comparing body side skin at the August time point to the December one (A/D) in Aohan fine wool sheep. Then seven differentially expressed genes were selected to validated the reliability of the gene chip data. The majority of the genes possibly related to follicle development and wool growth could be assigned into the categories including regulation of receptor binding, extracellular region, protein binding and extracellular space. Proteomic study revealed that 84 protein spots showed significant differences in expression levels. Of the 84, 63 protein spots were upregulated and 21 were downregulated in A/D. Finally, 55 protein points were determined through MALDI-TOF/MS analyses. Furthermore, the regulation mechanism of hair follicle might resemble that of fetation.
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Affiliation(s)
- Nan Liu
- Qingdao Agricultural University, Qingdao, 266109, China,
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16
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Magalhães-Padilha DM, Geisler-Lee J, Wischral A, Gastal MO, Fonseca GR, Eloy YRG, Geisler M, Figueiredo JR, Gastal EL. Gene Expression During Early Folliculogenesis in Goats Using Microarray Analysis. Biol Reprod 2013; 89:19. [PMID: 23759311 DOI: 10.1095/biolreprod.112.106096] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Understanding of gene expression and metabolic, biological and physiological pathways in ovarian follicular development can have a significant impact on the dynamics of follicular atresia or survival. In fact, some oocyte loss occurs during the transition from secondary to early tertiary follicles. This study aimed to understand, by microarray analysis, the temporal changes in transcriptional profiles of secondary and early antral (tertiary) follicles in caprine ovaries. Ovarian follicles were microdissected and pooled to extract total RNA. The RNA was cross hybridized with the bovine array. Among 23,987 bovine genes, a total of 14,323 genes were hybridized with goat mRNAs while 9,664 genes were not. Of all the hybridized genes, 2,466 were stage-specific, up- and down-regulated in the transition from secondary to early tertiary follicles. Gene expression profiles showed that three major metabolic pathways (lipid metabolism, cell death, and hematological system) were significantly differentiated between the two follicle stages. In conclusion, this study has identified important genes and pathways which may potentially be involved in the transition from secondary to early tertiary follicles in goats.
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17
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Brenaut P, Bangera R, Bevilacqua C, Rebours E, Cebo C, Martin P. Validation of RNA isolated from milk fat globules to profile mammary epithelial cell expression during lactation and transcriptional response to a bacterial infection. J Dairy Sci 2012; 95:6130-44. [PMID: 22921620 DOI: 10.3168/jds.2012-5604] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 05/22/2012] [Indexed: 12/12/2022]
Abstract
Mastitis, an inflammation of the mammary gland, is the most costly infectious disease of dairy ruminants worldwide. Although it receives considerable attention, the early steps of the host response remain poorly defined. Here, we report a noninvasive method using milk fat globules (MFG) as a source of mammary RNA to follow the dynamics of the global transcriptional response of mammary epithelial cells (MEC) during the course of a bacterial infection. We first assessed that RNA isolated from MFG were representative of MEC RNA; we then evaluated whether MFG RNA could be used to monitor the MEC response to infection. Sufficiently high yields of good-quality RNA (RNA integrity numbers ranging between 6.7 and 8.7) were obtained from goat MFG for subsequent analyses. Contamination of MFG by macrophages and neutrophils, which can be trapped during creaming, was assessed and when using quantitative real-time PCR for cell-type specific markers, was shown to be weak enough (<8%) to affect MFG gene expression profiling. Using microarrays, we showed that RNA extracted from MFG and from mammary alveolar parenchyma shared approximately 90% of the highlighted probes corresponding in particular to genes encoding milk proteins (CSN, BLG, LALBA) and enzymes involved in milk fat synthesis and secretion (FASN, XDH, ADRP, SCD, and DGAT1). In addition, a gene involved in the acute-phase reaction, coding for the serum amyloid A3 (SAA3) protein, was found within the first 50 most highly expressed genes in a noninfectious context in both mammary alveolar parenchyma and MFG, strongly suggesting that SAA3 is expressed in MEC. We took advantage of this noninvasive RNA sampling to follow the early proinflammatory response of MEC during the course of a bacterial infection and showed that the levels of mRNA encoding SAA3 sharply increased at 24h postinfection. Taken together, our results demonstrate that MFG represent a unique source of MEC RNA to noninvasively sample sufficient amounts of high-quality RNA to assess the dynamics of MEC gene expression in vivo, especially during the first steps of infection, thereby paving the way for the discovery of early biomarkers for the control of intramammary infections. Furthermore, this noninvasive technique could be used to provide mammary transcriptomic data on a large scale, thus filling the gap between genomic and phenotypic data.
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Affiliation(s)
- P Brenaut
- INRA, UMR1313 Unité Génétique Animale et Biologie Intégrative, équipe «Lait, Génome & Santé» F-78350 Jouy-en-Josas, France
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Dhorne-Pollet S, Robert-Granié C, Aurel MR, Marie-Etancelin C. A functional genomic approach to the study of the milking ability in dairy sheep. Anim Genet 2011; 43:199-209. [PMID: 22404356 DOI: 10.1111/j.1365-2052.2011.02237.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To understand the mechanisms underlying milk ability and more precisely the kinetics of milk emission, we compared teat transcriptome profiles from Lacaune ewes in the tails of the milk flow phenotypic distribution. Two different arrays containing respectively 1896 and 13 168 PCR products selected from several tissue-specific cDNA libraries, including mammary gland, allowed the identification of 73 differentially expressed genes between teats from high and low milk flow ewes. Genes involved in muscle contraction were identified as over-expressed, and genes encoding collagen were found to be under-expressed in teats from low milk flow ewes. We confirmed this underexpression of COL1A1 and COL1A2 in low-milk flow ewes using RT-qPCR. These results suggest that milking ability may be due to the capacity of the teat sphincter to relax during mechanical milking. We propose that an optimal condition for mechanical milking may require proper relaxation of the teats. To our knowledge, this is the first transcriptomic analysis studying milking ability, using udder tissue for gene expression profiling, which demonstrates that mechanical milking ability is not only determined by morphological features but also by tissue composition.
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Affiliation(s)
- S Dhorne-Pollet
- UMR 1313-Génétique Animale et Biologie Intégrative, Plateforme d'instrumentation et de Compétences en Transcriptomique, Jouy-en-Josas, France.
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Darby BJ, Jones KL, Wheeler D, Herman MA. Normalization and centering of array-based heterologous genome hybridization based on divergent control probes. BMC Bioinformatics 2011; 12:183. [PMID: 21600029 PMCID: PMC3125262 DOI: 10.1186/1471-2105-12-183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 05/21/2011] [Indexed: 11/21/2022] Open
Abstract
Background Hybridization of heterologous (non-specific) nucleic acids onto arrays designed for model-organisms has been proposed as a viable genomic resource for estimating sequence variation and gene expression in non-model organisms. However, conventional methods of normalization that assume equivalent distributions (such as quantile normalization) are inappropriate when applied to non-specific (heterologous) hybridization. We propose an algorithm for normalizing and centering intensity data from heterologous hybridization that makes no prior assumptions of distribution, reduces the false appearance of homology, and provides a way for researchers to confirm whether heterologous hybridization is suitable. Results Data are normalized by adjusting for Gibbs free energy binding, and centered by adjusting for the median of a common set of control probes assumed to be equivalently dissimilar for all species. This procedure was compared to existing approaches and found to be as successful as Loess normalization at detecting sequence variations (deletions) and even more successful than quantile normalization at reducing the accumulation of false positive probe matches between two related nematode species, Caenorhabditis elegans and C. briggsae. Despite the improvements, we still found that probe fluorescence intensity was too poorly correlated with sequence similarity to result in reliable detection of matching probe sequence. Conclusions Cross-species hybridizations can be a way to adapt genome-enabled tools for closely related non-model organisms, but data must be appropriately normalized and centered in a way that accommodates hybridization of nucleic acids with diverged sequence. For short, 25-mer probes, hybridization intensity alone may be insufficiently correlated with sequence similarity to allow reliable inference of homology at the probe level.
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Affiliation(s)
- Brian J Darby
- Ecological Genomics Institute, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
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Roy NC, Altermann E, Park ZA, McNabb WC. A comparison of analog and Next-Generation transcriptomic tools for mammalian studies. Brief Funct Genomics 2011; 10:135-50. [DOI: 10.1093/bfgp/elr005] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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21
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Bevilacqua C, Makhzami S, Helbling JC, Defrenaix P, Martin P. Maintaining RNA integrity in a homogeneous population of mammary epithelial cells isolated by Laser Capture Microdissection. BMC Cell Biol 2010; 11:95. [PMID: 21134253 PMCID: PMC3019183 DOI: 10.1186/1471-2121-11-95] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 12/06/2010] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Laser-capture microdissection (LCM) that enables the isolation of specific cell populations from complex tissues under morphological control is increasingly used for subsequent gene expression studies in cell biology by methods such as real-time quantitative PCR (qPCR), microarrays and most recently by RNA-sequencing. Challenges are i) to select precisely and efficiently cells of interest and ii) to maintain RNA integrity. The mammary gland which is a complex and heterogeneous tissue, consists of multiple cell types, changing in relative proportion during its development and thus hampering gene expression profiling comparison on whole tissue between physiological stages. During lactation, mammary epithelial cells (MEC) are predominant. However several other cell types, including myoepithelial (MMC) and immune cells are present, making it difficult to precisely determine the specificity of gene expression to the cell type of origin. In this work, an optimized reliable procedure for producing RNA from alveolar epithelial cells isolated from frozen histological sections of lactating goat, sheep and cow mammary glands using an infrared-laser based Arcturus Veritas LCM (Applied Biosystems®) system has been developed. The following steps of the microdissection workflow: cryosectioning, staining, dehydration and harvesting of microdissected cells have been carefully considered and designed to ensure cell capture efficiency without compromising RNA integrity. RESULTS The best results were obtained when staining 8 μm-thick sections with Cresyl violet® (Ambion, Applied Biosystems®) and capturing microdissected cells during less than 2 hours before RNA extraction. In addition, particular attention was paid to animal preparation before biopsies or slaughtering (milking) and freezing of tissue blocks which were embedded in a cryoprotective compound before being immersed in isopentane. The amount of RNA thus obtained from ca.150 to 250 acini (300,000 to 600,000 μm2) ranges between 5 to 10 ng. RNA integrity number (RIN) was ca. 8.0 and selectivity of this LCM protocol was demonstrated through qPCR analyses for several alveolar cell specific genes, including LALBA (α-lactalbumin) and CSN1S2 (αs2-casein), as well as Krt14 (cytokeratin 14), CD3e and CD68 which are specific markers of MMC, lymphocytes and macrophages, respectively. CONCLUSIONS RNAs isolated from MEC in this manner were of very good quality for subsequent linear amplification, thus making it possible to establish a referential gene expression profile of the healthy MEC, a useful platform for tumor biomarker discovery.
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Affiliation(s)
- Claudia Bevilacqua
- INRA, UMR1313 Unité Génétique Animale et Biologie Intégrative, équipe Lait, Génome & Santé F-78350 Jouy-en-Josas, France.
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