GSE121808
Enhancer associated long non-coding RNA transcription and immune gene regulation in experimental models of rickettsial infection
Recent discovery that much of the mammalian genome does not encode protein-coding genes (PCGs) has brought widespread  attention to long noncoding RNAs (lncRNAs) as a novel layer of biological regulation. Enhancer lnc (elnc) RNAs from the enhancer  regions of the genome carry the capacity to regulate PCGs in cis or in trans. Spotted fever rickettsioses represent the  consequence of host infection with Gram-negative, obligate intracellular bacteria in the Genus Rickettsia. Despite being implicated  in the pathways of infection and inflammation, the roles of lncRNAs in host response to Rickettsia species have remained a  mystery. We have profiled the expression of host lncRNAs during infection of susceptible mice with R. conorii as a model closely  mimicking the pathogenesis of human spotted fever rickettsioses. RNA sequencing on the lungs of infected hosts yielded reads  mapping to 74,964 non-coding RNAs, 206 and 277 of which were determined to be significantly up- and down-regulated in  comparison to uninfected controls. Following removal of short non-coding RNAs and ambiguous transcripts, remaining transcripts  underwent in-depth analysis of mouse lung epigenetic signatures H3K4Me1 and H3K4Me3, active transcript markers (POLR2A, p300,  CTCF), and DNaseI hypersensitivity sites to identify two potentially active and highly up-regulated elncRNAs NONMMUT013718 and  NONMMUT024103. Using Hi-3C sequencing resource, we further determined that genomic loci of NONMMUT013718 and  NONMMUT024103 might interact with and regulate the expression of nearby PCGs, namely Id2 (inhibitor of DNA binding 2) and  Apol10b (apolipoprotein 10b), respectively. Heterologous reporter assays confirmed the activity of elncRNAs as the inducers of  their predicted PCGs. In the lungs of infected mice, expression of both elncRNAs and their targets was significantly higher than  mock-infected controls. Induced expression of NONMMUT013718/Id2 in murine macrophages and NONMMUT024103/Apol10b in  endothelial cells was also clearly evident during R. conorii infection in vitro. Finally, shRNA mediated knock-down of  NONMMUT013718 and NONMMUT024103 elncRNAs resulted in reduced expression of endogenous Id2 and Apl10b, demonstrating the  regulatory roles of these elncRNAs on their target PCGs. Our results provide very first experimental evidence suggesting altered  expression of pulmonary lncRNAs and elncRNA-mediated regulation of PCGs involved in immunity and during host interactions with  pathogenic rickettsiae. Overall design: Examination of expression of long non coding RNA's in mice infected with R. conorii in comparison to non infected mice.