1. CRISPR/Cas-based screening of long non-coding RNAs (lncRNAs) in macrophages with an NF-κB reporter
- Author
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Covarrubias, Sergio, Robinson, Elektra K, Shapleigh, Barbara, Vollmers, Apple, Katzman, Sol, Hanley, Nicole, Fong, Nicholas, McManus, Michael T, and Carpenter, Susan
- Subjects
Biological Sciences ,Medicinal and Biomolecular Chemistry ,Chemical Sciences ,Genetics ,Biotechnology ,2.1 Biological and endogenous factors ,Aetiology ,Inflammatory and immune system ,Animals ,CRISPR-Cas Systems ,Cells ,Cultured ,Cyclooxygenase 2 ,Gene Knockout Techniques ,Genes ,Reporter ,Green Fluorescent Proteins ,Humans ,Immunity ,Innate ,Macrophages ,Mice ,NF-kappa B ,RNA ,Long Noncoding ,Recombinant Fusion Proteins ,Signal Transduction ,CRISPR/Cas ,NF-κB ,inflammation ,long non-coding RNA ,macrophage ,toll-like receptor ,Medical and Health Sciences ,Biochemistry & Molecular Biology ,Biological sciences ,Biomedical and clinical sciences ,Chemical sciences - Abstract
The innate immune system protects against infections by initiating an inducible inflammatory response. NF-κB is one of the critical transcription factors controlling this complex response, but some aspects of its regulation remain unclear. For example, although long non-coding RNAs (lncRNAs) have been shown to critically regulate gene expression, only a fraction of these have been functionally characterized, and the extent to which lncRNAs control NF-κB expression is unknown. Here, we describe the generation of a GFP-based NF-κB reporter system in immortalized murine bone marrow-derived macrophages (iBMDM). Activation of this reporter, using Toll-like receptor ligands, resulted in GFP expression, which could be monitored by flow cytometry. We also established a CRISPR/Cas9 gene deletion system in this NF-κB reporter line, enabling us to screen for genes that regulate NF-κB signaling. Our deletion-based approach identified two long intergenic non-coding(linc)RNAs, lincRNA-Cox2 and lincRNA-AK170409, that control NF-κB signaling. We demonstrate a potential novel role for lincRNA-Cox2 in promoting IκBα degradation in the cytoplasm. For lincRNA-AK170409, we provide evidence that this nuclearly-localized lincRNA regulates a number of inflammation-related genes. In conclusion, we have established an NF-κB-GFP iBMDM reporter cell line and a line that stably expresses Cas9. Our approach enabled the identification of lincRNA-Cox2 and lincRNA-AK170409 as NF-κB regulators, and this tool will be useful for identifying additional genes involved in regulating this transcription factor critical for immune function.
- Published
- 2017