The regulation of COX-2, ABCA1 and ABCG1 by the lncRNA PACERR links the inflammatory response and cholesterol homeostasis

The COX-2 antisense lncRNA PACERR interacts with discrete RNA binding proteins to mediate a cell specific COX-2 response to HDL. PACERR exerts its action both in cis and in trans, controlling the expression of COX-2 in macrophages, while also regulating the levels of macrophage ABCA1 and ABCG1, cholesterol transport genes involved in maintaining cholesterol homeostasis. When cells are exposed to HDL, PACERR is transcribed, leading to the release of bound histone acetyltransferase p300 and its relocation to the promoter of COX-2 which is then transcribed, leading to PG formation. In concert, PACERR also releases heterogeneous nuclear ribonucleoprotein L (hnRNPL) which relocates to the ABCA1 and ABCG1 gene loci, controlling mRNA alternative splicing and subsequent cholesterol efflux to HDL. A strong hnRNPL binding site motif is found in PACERR RNA and when this was deleted, the interaction between PACERR RNA and hnRNPL is abrogated both at baseline and following HDL treatment of macrophages. THP-1 macrophages stably overexpressing PACERR (P1-3) or deleted of the hnRNPL binding site (Delta1-3) from the PACERR sequence. In delta cells, PACERR no longer binds to hnRNPL but is free to bind to ABCA1 and ABCG1 impacting their transcription. In summary, we found that PACERR controls the levels of the cholesterol transporters through its interaction with the splicing factor, hnRNPL. It is released from PACERR RNA in response to HDL where it relocates to introns of cholesterol transporters determining the alternative splicing fate of transcripts required for cholesterol efflux. Through use of the delta cells, we have Illustrated the specificity for the interaction between hnRNPL and PACERR.