Abstract P1147: Cardinal Is A Nuclear Lncrna That Represses SRF/TCF-mediated Gene Transcription By Co-occupying SRF/TCF-bound Gene Promoters In The Heart

Abstract

LncRNAs are an emerging class of co-transcriptional regulators important for balancing gene expression networks in the heart during development and disease. We recently characterized a cardiac-specific lncRNA named CARDINAL, which is transcribed adjacent to the SRF-coactivator myocardin. Myocardin, and members of the ternary complex factor (TCF) family (Elk1-4), compete for interaction with SRF to balance opposing transcriptional networks in the heart. Previously we showed that CARDINAL forms a stable complex with SRF and can repress SRF/TCF-mediated gene transcription, suggesting CARDINAL functions as an RNA cofactor for SRF. Here we show using RNAscope in situ hybridization that CARDINAL is a nuclear lncRNA in both mouse and human cardiomyocytes. To identify CARDINAL-regulated genes, we performed Chromatin Isolation by RNA Purification (ChIRP) using anti-sense oligonucleotides specific to endogenous CARDINAL in HL-1 cardiomyocytes, followed by deep sequencing. CARDINAL transcripts were localized at ~100 genes, with the majority (76%) of CARDINAL peaks occupying the transcriptional start site (TSS) of gene promoters. Strikingly, the majority of CARDINAL ChIRP peaks overlapped with SRF-bound ChIP peaks in the cardiac genome. Homer motif analyses of CARDINAL peaks identified enrichment for the SRF CArG box and TCF binding motifs for Elk1 and Elk4. Consistent with our previous findings, CARDINAL peaks were localized to canonical SRF/TCF-regulated genes, including Egr1, Elk4, and components of the AP-1 complex, such as c-Fos, Junb, and Jund. These findings highlight CARDINAL, similar to its protein coding neighbor gene myocardin, as a co-regulator of SRF-dependent gene transcription. CARDINAL, however, in contrast to myocardin, can repress SRF/TCF-dependent gene transcription, which is likely mediated by its unique ability to co-occupy SRF/TCF-bound gene promoters.