title: Dual RNA sequencing reveals the expression of unique transcriptomic signatures in lipopolysaccharide-induced BV-2 microglial cells.
abstract: Microglial cells become rapidly activated through interactions with pathogens, and the persistent activation of these cells is associated with various neurodegenerative diseases. Previous studies have investigated the transcriptomic signatures in microglia or macrophages using microarray technologies. However, this method has numerous restrictions, such as spatial biases, uneven probe properties, low sensitivity, and dependency on the probes spotted. To overcome this limitation and identify novel transcribed genes in response to LPS, we used RNA Sequencing (RNA-Seq) to determine the novel transcriptomic signatures in BV-2 microglial cells. Sequencing assessment and quality evaluation showed that approximately 263 and 319 genes (≥ 1.5 log2-fold), such as cytokines and chemokines, were strongly induced after 2 and 4 h, respectively, and the induction of several genes with unknown immunological functions was also observed. Importantly, we observed that previously unidentified transcription factors (TFs) (irf1, irf7, and irf9), histone demethylases (kdm4a) and DNA methyltransferases (dnmt3l) were significantly and selectively expressed in BV-2 microglial cells. The gene expression levels, transcription start sites (TSS), isoforms, and differential promoter usage revealed a complex pattern of transcriptional and post-transcriptional gene regulation upon infection with LPS. In addition, gene ontology, molecular networks and pathway analyses identified the top significantly regulated functional classification, canonical pathways and network functions at each activation status. Moreover, we further analyzed differentially expressed genes to identify transcription factor (TF) motifs (-950 to +50 bp of the 5' upstream promoters) and epigenetic mechanisms. Furthermore, we confirmed that the expressions of key inflammatory genes as well as pro-inflammatory mediators in the supernatants were significantly induced in LPS treated primary microglial cells. This transcriptomic analysis is the first to show a comparison of the family-wide differential expression of most known immune genes and also reveal transcription evidence of multiple gene families in BV-2 microglial cells. Collectively, these findings reveal unique transcriptomic signatures in BV-2 microglial cells required for homeostasis and effective immune responses.
authors: Department of Bionanotechnology, Hanyang University, Seoul, Republic of Korea.
authors: Amitabh
authors: A
authors: Das
authors: Department of Molecular & Life Sciences, Hanyang University, Ansan, Republic of Korea.
authors: Jin Choul
authors: JC
authors: Chai
authors: Department of Molecular & Life Sciences, Hanyang University, Ansan, Republic of Korea.
authors: Sun Hwa
authors: SH
authors: Kim
authors: Department of Molecular & Life Sciences, Hanyang University, Ansan, Republic of Korea.
authors: Kyoung Sun
authors: KS
authors: Park
authors: Department of Molecular & Life Sciences, Hanyang University, Ansan, Republic of Korea.
authors: Young Seek
authors: YS
authors: Lee
authors: Institute of Natural Science & Technology, Hanyang University, Ansan, Republic of Korea.
authors: Kyoung Hwa
authors: KH
authors: Jung
authors: Department of Bionanotechnology, Hanyang University, Seoul, Republic of Korea; Department of Molecular & Life Sciences, Hanyang University, Ansan, Republic of Korea.
authors: Young Gyu
authors: YG
authors: Chai
mesh_terms: D016229:Amyloid beta-Peptides / Q000378:metabolism; D000818:Animals; D016207:Cytokines / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic / Q000187:drug effects; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks / Q000187:drug effects; D007249:Inflammation / Q000235:genetics; D018836:Inflammation Mediators / Q000378:metabolism; D008070:Lipopolysaccharides / Q000494:pharmacology*; D051379:Mice; D017628:Microglia / Q000187:drug effects / Q000378:metabolism*; D010446:Peptide Fragments / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*; D015398:Signal Transduction / Q000187:drug effects / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic / Q000187:drug effects; D059467:Transcriptome / Q000235:genetics*
chemical_list: D016229:Amyloid beta-Peptides; D016207:Cytokines; D018836:Inflammation Mediators; D008070:Lipopolysaccharides; D010446:Peptide Fragments; D012333:RNA, Messenger; D014157:Transcription Factors; C075222:amyloid beta-protein (1-42)