(A) SDS-PAGE analysis of proteins purified from in vitro binding assay using biotinylated lincRNA-EPS or antisense control RNA, and macrophage nuclear extracts. The highlighted protein bands were subjected to Mass Spectrometry analysis.
(B) Western blot confirms lincRNA-EPS and hnRNPL interaction in vitro.
(C and D) hnRNPL RIP followed by RT-qPCR analysis of co-purified RNAs in non-cross-linked BMDMs (C) and formaldehyde cross-linked BMDMs (D). Immunoprecipitation of hnRNPL was assessed by western blot (inset, panel C).
(E) Western blot assessing the knockdown of hnRNPL in iBMDMs stably expressing shRNAs targeting non-overlapping regions of hnRNPL, and the control shRNA against GFP.
(F and G) Control iBMDMs or those expressing hnRNPL specific shRNAs were stimulated with LPS, and subjected to RT-qPCR analysis of Cxcl10 mRNA (F), and ELISA against Cxcl10 protein levels (G).
(H) RT-qPCR analysis of unspliced and spliced forms of lincRNA-EPS in iBMDMs expressing control or hnRNPL specific shRNAs. *, p < 0.05.
(I) Schematic of lincRNA-EPS deletion mutants used in RNA-protein binding assays.
(J) hnRNPL binds 3′-region of lincRNA-EPS. In vitro RNA: protein binding assay was performed using biotinylated full-length or deletion mutants of lincRNA-EPS and the nuclear extracts isolated from BMDMs, captured using streptavidin beads, and subjected to western blot against hnRNPL.
(K) The 3′-region (2000 – 2531 nt) of lincRNA-EPS is necessary and sufficient to suppress Cxcl10 expression. lincRNA-EPS−/− iBMDMs expressing full-length or deletion mutants of lincRNA-EPS were stimulated with LPS for 6 hr, and mRNA levels analyzed by RT-qPCR. *, p < 0.05; **, p < 0.01.
(L) Schematic of CANACA motifs in the 3′-region (2000 – 2531 nt) of lincRNA-EPS. The nucleotide mutations in CANACA tracts are highlighted.
(M) lincRNA-EPS binds hnRNPL through a CANACA motif (2386 – 2391 nt) embedded in its 3′-region. In vitro RNA: protein binding assay was performed using biotinylated WT or CANACA tract mutant versions of the full-length lincRNA-EPS, captured using streptavidin beads, and subjected to western blot against hnRNPL.
(N) Functional role of CANACA motif (2386 – 2391 nt) of lincRNA-EPS. lincRNA-EPS−/− BMDMs expressing WT or the point mutants of the full-length lincRNA-EPS (defective in hnRNPL binding) were stimulated with LPS for 6 hr, and mRNA levels analyzed by RT-qPCR. **, p < 0.01.
See also .