Cardiovascular Disease and Long Noncoding RNAs

Abstract

T he last decade has ushered in a surge of genetic information with budget-friendly and more efficient sequencing technologies adding to our understanding of human development and disease. The sequencing of the human genome was a remarkable feat, yet using this information to understand human health and disease has proven to be challenging. The mammalian genome is comprised of a complex infrastructure of defined nucleotide sequences and dynamic epigenetic modifications that result in shifts in gene expression patterns and subsequent developmental and phenotypic outcomes. Genome wide association studies (GWAS) have demonstrated the link between alterations in nucleotide sequences created by mutations , such as single nucleotide polymorphisms (SNPs) and disease. However, it remains unclear how SNPs alter gene expression patterns and phenotypes. One hypothesis links SNP containing regions to mutational phenotypes via changes to epigenetic processes that control how genes are regulated, such as DNA methylation and histone acetylation. SNPs are changes in nucleotide sequences that occur in at least 1% of the population. It is estimated that there are 10 to 30 million SNPs in humans that occur every 100 to 300 bases, and this variation is the major source of heterogeneity among people. A nonsynonymous SNP changes the amino acid sequence of a protein-coding gene. Less than 10% of SNPs are nonsyn-onymous, whereas 90% occur in nonprotein coding regions of the genome. 1 SNPs can be found in regions of deoxyribo-nuclease I (DNase I) hypersensitivity or promoters affecting transcription factor-binding sites and chromatin state. SNPs can create or delete microRNA-binding sites in 3ʹ untranslated regions (UTRs) affecting microRNA target mRNA expression. 2 SNPs can also be found in regions expressing noncoding RNAs, such as long noncoding RNAs (lncRNAs) leading to alterations in their expression patterns. SNPs can affect alternative splicing and the secondary structure of an RNA transcript leading to altered function (Figure 1). It has been estimated that 7% of SNPs that associate with autoimmune diseases are found in lncRNAs located in intergenic regions, signifying the increasing importance of these noncoding regions. 3 LncRNAs represent undiscovered disease-associated loci that could be identified through GWAS analysis. The National Institutes of Health sponsored ENCODE (Encyclopedia of DNA Elements) project set out to uncover all of the functional elements of the human genome. It revealed that 85% of the human genome is transcribed into several classes of noncoding RNAs, whereas only 3% is translated into protein. 4,5 RNA-sequencing (RNA-seq) is currently the most widespread method for detecting the expression of RNA transcripts and for identifying novel noncoding transcripts. 6