Cell type-specific expression of endogenous cardiac Troponin I antisense RNA in the neonatal rat heart

Right ventricular long noncoding RNA expression in human heart failure

The expression of long noncoding RNAs (lncRNAs) in human heart failure (HF) has not been widely studied. Using RNA sequencing (RNA-Seq), we compared lncRNA expression in 22 explanted human HF hearts with lncRNA expression in 5 unused donor human hearts. We used Cufflinks to identify isoforms and DESeq to identify differentially expressed genes. We identified the noncoding RNAs by cross-reference to Ensembl release 73 (Genome Reference Consortium human genome build 37) and explored possible functional roles using a variety of online tools. In HF hearts, RNA-Seq identified 84,793 total messenger RNA coding and noncoding different transcripts, including 13,019 protein-coding genes, 2,085 total lncRNA genes, and 1,064 pseudogenes. By Ensembl noncoding RNA categories, there were 48 lncRNAs, 27 pseudogenes, and 30 antisense RNAs for a total of 105 differentially expressed lncRNAs in HF hearts. Compared with donor hearts, HF hearts exhibited differential expression of 7.7% of protein-coding genes, 3.7% of lncRNAs (including pseudogenes), and 2.5% of pseudogenes. There were not consistent correlations between antisense lncRNAs and parent genes and between pseudogenes and parent genes, implying differential regulation of expression. Exploratory in silico functional analyses using online tools suggested a variety of possible lncRNA regulatory roles. By providing a comprehensive profile of right ventricular polyadenylated messenger RNA transcriptome in HF, RNA-Seq provides an inventory of differentially expressed lncRNAs, including antisense transcripts and pseudogenes, for future mechanistic study.

Interplay of chromatin modifications and non-coding RNAs in the heart

Precisely regulated patterns of gene expression are dependent on the binding of transcription factors and chromatin-associated determinants referred to as co-activators and co-repressors. These regulatory components function with the core transcriptional machinery to serve in critical activities to alter chromatin modification and regulate gene expression. While we are beginning to understand that cell-type specific patterns of gene expression are necessary to achieve selective cardiovascular developmental programs, we still do not know the molecular machineries that localize these determinants in the heart. With clear implications for the epigenetic control of gene expression signatures, the ENCODE (Encyclopedia of DNA Elements) Project Consortium determined that about 90% of the human genome is transcribed while only 1-2% of transcripts encode proteins. Emerging evidence suggests that non-coding RNA (ncRNA) serves as a signal for decoding chromatin modifications and provides a potential molecular basis for cell type-specific and promoter-specific patterns of gene expression. The discovery of the histone methyltransferase enzyme EZH2 in the regulation of gene expression patterns implicated in cardiac hypertrophy suggests a novel role for chromatin-associated ncRNAs and is the focus of this article.