Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice

Abstract

Sequence polymorphisms in a 58kb interval on chromosome 9p21 confer a markedly increased risk for coronary artery disease (CAD), the leading cause of death worldwide 1,2. The variants have a substantial impact on the epidemiology of CAD and other life-threatening vascular conditions since nearly a quarter of Caucasians are homozygous for risk alleles. However, the risk interval is devoid of protein-coding genes and the mechanism linking the region to CAD risk has remained enigmatic. Here we show that deletion of the orthologous 70kb noncoding interval on mouse chromosome4 affects cardiac expression of neighboring genes, as well as proliferation properties of vascular cells. Chr4Δ70kb/Δ70kb mice are viable, but show increased mortality both during development and as adults. Cardiac expression of two genes near the noncoding interval, Cdkn2a and Cdkn2b, is severely reduced in chr4Δ70kb/Δ70kb mice, indicating that distant-acting gene regulatory functions are located in the noncoding CAD risk interval. Allele-specific expression of Cdkn2b transcripts in heterozygous mice revealed that the deletion affects expression through a cis-acting mechanism. Primary cultures of chr4Δ70kb/Δ70kb aortic smooth muscle cells exhibited excessive proliferation and diminished senescence, a cellular phenotype consistent with accelerated CAD pathogenesis. Taken together, our results provide direct evidence that the CAD risk interval plays a pivotal role in regulation of cardiac Cdkn2a/b expression and suggest that this region affects CAD progression by altering the dynamics of vascular cell proliferation.

Long noncoding RNA in genome regulation

“…21 Targeted deletion of the orthologous 70 kb region in a mouse model altered cardiac transcript levels of neighboring genes Cdkn2A and Cdkn2b and resulted in aberrant cell proliferation. 22 Thus, an lncRNA locus may provide a mechanistic link between a disease polymorphism and its associated phenotype.…”

9p21 Polymorphisms increase the risk of peripheral artery disease in the Han Chinese population

“…Functional studies have demonstrated that 9p21 contributes to CAD via atherosclerosis induced by variants located near CDKN2A, CDKN2B and CDKN2B antisense RNA 1 (CDKN2B-AS1) genes, which are involved in regulating cell proliferation, cell ageing and senescence, and apoptosis. 16,[30][31][32][33] Other research found that 9p21 contributed to CAD development by modulating the inflammatory pathway involved in the atherosclerosis process, 34 or by deposition of coronary artery atheroma. 13,35 Despite these data, the mechanism of the interaction between 9p21 and PAD requires further investigation.…”

Macro lncRNAs

“…3C) and the deletion of the orthologous 70 kb region on mouse chromosome 7 showed that expression levels of p16 INK4A and p15 INK4B are markedly reduced in cis. 102 Despite the existence of at least eight non-coding splice variants, 101 the functions of unspliced ANRIL in regulating p15 INK4B in cis cannot be dismissed. 91 …”