TY - JOUR
T1 - Profiling microRNA expression in bovine alveolar macrophages using RNA-seq
AU - Vegh, Peter
AU - Foroushani, Amir B K
AU - Magee, David A.
AU - McCabe, Matthew S.
AU - Browne, John A.
AU - Nalpas, Nicolas C.
AU - Conlon, Kevin M.
AU - Gordon, Stephen V.
AU - Bradley, Daniel G.
AU - MacHugh, David E.
AU - Lynn, David J.
N1 - Funding Information:
This project was funded by Teagasc (RMIS 6082), an Investigator Grant from Science Foundation Ireland ( SFI/08/IN.1/B2038 ) and a Research Stimulus Grant from the Department of Agriculture, Food and the Marine ( RSF 06 405 ). Amir B.K. Foroushani and Peter Vegh are supported by a Teagasc Walsh Fellowship. We thank Dr. Eddie Jordan (UCD Lyons Research Farm), Dr. Joseph Cassidy, Mr. Brian Cloak, Ms. Claire Healy, Ms. Kirsten McLoughlin and Ms. Jing Chen (all UCD Veterinary Sciences Centre) for assistance with animal procurement and lung lavages. We also thank Dr. George Cloughley, Ms. Bernadette Legget, Mrs. Yvonne Abbott and Mrs. Maureen McCullough for assistance with microbial testing of samples (all UCD Veterinary Sciences Centre). The sequencing service was provided by the Norwegian Sequencing Centre ( www.sequencing.uio.no ), a national technology platform hosted by the University of Oslo and supported by the “Functional Genomics” and “Infrastructure” programs of the Research Council of Norway and the Southeastern Regional Health Authorities.
PY - 2013/10/1
Y1 - 2013/10/1
N2 - MicroRNAs (miRNAs) are important regulators of gene expression and are known to play a key role in regulating both adaptive and innate immunity. Bovine alveolar macrophages (BAMs) help maintain lung homeostasis and constitute the front line of host defense against several infectious respiratory diseases, such as bovine tuberculosis. Little is known, however, about the role miRNAs play in these cells. In this study, we used a high-throughput sequencing approach, RNA-seq, to determine the expression levels of known and novel miRNAs in unchallenged BAMs isolated from lung lavages of eight different healthy Holstein-Friesian male calves. Approximately 80 million sequence reads were generated from eight BAM miRNA Illumina sequencing libraries, and 80 miRNAs were identified as being expressed in BAMs at a threshold of at least 100 reads per million (RPM). The expression levels of miRNAs varied over a large dynamic range, with a few miRNAs expressed at very high levels (up to 800,000. RPM), and the majority lowly expressed. Notably, many of the most highly expressed miRNAs in BAMs have known roles in regulating immunity in other species (e.g. bta-let-7i, bta-miR-21, bta-miR-27, bta-miR-99b, bta-miR-146, bta-miR-147, bta-miR-155 and bta-miR-223). The most highly expressed miRNA in BAMs was miR-21, which has been shown to regulate the expression of antimicrobial peptides in Mycobacterium leprae-infected human monocytes. Furthermore, the predicted target genes of BAM-expressed miRNAs were found to be statistically enriched for roles in innate immunity. In addition to profiling the expression of known miRNAs, the RNA-seq data was also analysed to identify potentially novel bovine miRNAs. One putatively novel bovine miRNA was identified. To the best of our knowledge, this is the first RNA-seq study to profile miRNA expression in BAMs and provides an important reference dataset for investigating the regulatory roles miRNAs play in this important immune cell type.
AB - MicroRNAs (miRNAs) are important regulators of gene expression and are known to play a key role in regulating both adaptive and innate immunity. Bovine alveolar macrophages (BAMs) help maintain lung homeostasis and constitute the front line of host defense against several infectious respiratory diseases, such as bovine tuberculosis. Little is known, however, about the role miRNAs play in these cells. In this study, we used a high-throughput sequencing approach, RNA-seq, to determine the expression levels of known and novel miRNAs in unchallenged BAMs isolated from lung lavages of eight different healthy Holstein-Friesian male calves. Approximately 80 million sequence reads were generated from eight BAM miRNA Illumina sequencing libraries, and 80 miRNAs were identified as being expressed in BAMs at a threshold of at least 100 reads per million (RPM). The expression levels of miRNAs varied over a large dynamic range, with a few miRNAs expressed at very high levels (up to 800,000. RPM), and the majority lowly expressed. Notably, many of the most highly expressed miRNAs in BAMs have known roles in regulating immunity in other species (e.g. bta-let-7i, bta-miR-21, bta-miR-27, bta-miR-99b, bta-miR-146, bta-miR-147, bta-miR-155 and bta-miR-223). The most highly expressed miRNA in BAMs was miR-21, which has been shown to regulate the expression of antimicrobial peptides in Mycobacterium leprae-infected human monocytes. Furthermore, the predicted target genes of BAM-expressed miRNAs were found to be statistically enriched for roles in innate immunity. In addition to profiling the expression of known miRNAs, the RNA-seq data was also analysed to identify potentially novel bovine miRNAs. One putatively novel bovine miRNA was identified. To the best of our knowledge, this is the first RNA-seq study to profile miRNA expression in BAMs and provides an important reference dataset for investigating the regulatory roles miRNAs play in this important immune cell type.
KW - Alveolar macrophage
KW - Bovine
KW - MicroRNA
KW - RNA-seq
UR - http://www.scopus.com/inward/record.url?scp=84884590257&partnerID=8YFLogxK
U2 - 10.1016/j.vetimm.2013.08.004
DO - 10.1016/j.vetimm.2013.08.004
M3 - Article
C2 - 24021155
AN - SCOPUS:84884590257
SN - 0165-2427
VL - 155
SP - 238
EP - 244
JO - Veterinary Immunology and Immunopathology
JF - Veterinary Immunology and Immunopathology
IS - 4
ER -