Genetic Models Reveal cis and trans Immune-Regulatory Activities for lincRNA-Cox2
Roland Elling,
Elektra K. Robinson,
Barbara Shapleigh,
Stephen C. Liapis,
Sergio Covarrubias,
Sol Katzman,
Abigail F. Groff,
Zhaozhao Jiang,
Shiuli Agarwal,
Mona Motwani,
Jennie Chan,
Shruti Sharma,
Elizabeth J. Hennessy,
Garret A. FitzGerald,
Michael T. McManus,
John L. Rinn,
Katherine A. Fitzgerald,
Susan Carpenter
Affiliations
Roland Elling
Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA; Center for Pediatrics, Department of General Pediatrics, University of Freiburg, Freiburg, Germany
Elektra K. Robinson
Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
Barbara Shapleigh
Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
Stephen C. Liapis
Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
Sergio Covarrubias
Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
Sol Katzman
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
Abigail F. Groff
Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
Zhaozhao Jiang
Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
Shiuli Agarwal
Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
Mona Motwani
Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
Jennie Chan
Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
Shruti Sharma
Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
Elizabeth J. Hennessy
Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Smilow, Philadelphia, PA 19104, USA
Garret A. FitzGerald
Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Smilow, Philadelphia, PA 19104, USA
Michael T. McManus
Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA; UCSF Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
John L. Rinn
Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA; Department of Biochemistry, BioFrontiers, University of Colorado Boulder, Boulder, CO 80301, USA
Katherine A. Fitzgerald
Program in Innate Immunity, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
Susan Carpenter
Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA; Corresponding author
Summary: An inducible gene expression program is a hallmark of the host inflammatory response. Recently, long intergenic non-coding RNAs (lincRNAs) have been shown to regulate the magnitude, duration, and resolution of these responses. Among these is lincRNA-Cox2, a dynamically regulated gene that broadly controls immune gene expression. To evaluate the in vivo functions of this lincRNA, we characterized multiple models of lincRNA-Cox2-deficient mice. LincRNA-Cox2-deficient macrophages and murine tissues had altered expression of inflammatory genes. Transcriptomic studies from various tissues revealed that deletion of the lincRNA-Cox2 locus also strongly impaired the basal and inducible expression of the neighboring gene prostaglandin-endoperoxide synthase (Ptgs2), encoding cyclooxygenase-2, a key enzyme in the prostaglandin biosynthesis pathway. By utilizing different genetic manipulations in vitro and in vivo, we found that lincRNA-Cox2 functions through an enhancer RNA mechanism to regulate Ptgs2. More importantly, lincRNA-Cox2 also functions in trans, independently of Ptgs2, to regulate critical innate immune genes in vivo. : Elling et al. utilize a number of lincRNA-Cox2 genetic models to show that lincRNA-Cox2 can regulate its neighboring gene Ptgs2 (Cox2) through an enhancer RNA mechanism. They generate a lincRNA-Cox2 splicing-deficient mouse and confirm that lincRNA-Cox2 functions in trans to regulate immune genes following LPS-induced endotoxic shock. Keywords: lincRNA-Cox2, innate immunity, Ptgs2, inflammation, CRISPR/Cas9, CRISPRi
