Transcriptional Profiling of Hypoxia-Regulated Non-coding RNAs in Human Primary Endothelial Cells.

Pierre R Moreau,Minna U Kaikkonen,Nicholas L Downes,Henri Niskanen,Einari Aavik,Tiit Örd,Maria Bouvy-Liivrand,Seppo Ylä-Herttuala

doi:10.3389/fcvm.2018.00159

Abstract

Hypoxia occurs in human atherosclerotic lesions and has multiple adverse effects on endothelial cell metabolism. Recently, key roles of long non-coding RNAs (lncRNAs) in the development of atherosclerosis have begun to emerge. In this study, we investigate the lncRNA profiles of human umbilical vein endothelial cells subjected to hypoxia using global run-on sequencing (GRO-Seq). We demonstrate that hypoxia regulates the nascent transcription of ~1800 lncRNAs. Interestingly, we uncover evidence that promoter-associated lncRNAs are more likely to be induced by hypoxia compared to enhancer-associated lncRNAs, which exhibit an equal distribution of up- and downregulated transcripts. We also demonstrate that hypoxia leads to a significant induction in the activity of super-enhancers next to transcription factors and other genes implicated in angiogenesis, cell survival and adhesion, whereas super-enhancers near several negative regulators of angiogenesis were repressed. Despite the majority of lncRNAs exhibiting low detection in RNA-Seq, a subset of lncRNAs were expressed at comparable levels to mRNAs. Among these, MALAT1, HYMAI, LOC730101, KIAA1656, and LOC339803 were found differentially expressed in human atherosclerotic lesions, compared to normal vascular tissue, and may thus serve as potential biomarkers for lesion hypoxia.

Highlights

Recent transcriptomic analyses have established that up to 90% of the eukaryotic genome is transcribed [1]
To study the nascent transcriptomes of ncRNAs in primary human endothelial cells, we performed global run-on sequencing (GRO-Seq) on human umbilical vein endothelial cell (HUVEC) subjected to 8 h of hypoxia (1% oxygen)
We expand that list of long non-coding RNA (lncRNA) and contribute to the characterization of hypoxia-regulated lncRNAs in human primary endothelial cells

Summary

Introduction

Recent transcriptomic analyses have established that up to 90% of the eukaryotic genome is transcribed [1]. 2% of these transcripts encode for proteins, while the vast majority is transcribed as non-coding RNAs (ncRNAs). An increasing number of reports have discovered functional and structural roles for ncRNAs (e.g., microRNAs, small nucleolar RNAs, and small nucleolar RNAs), but despite this, the majority of them remain uncharacterized. The largest group of ncRNAs are called long ncRNAs (lncRNAs), which are defined as non-coding transcripts >200 nucleotides in length [2]. LncRNAs can be further divided into promoter-associated lncRNAs and enhancer-associated lncRNAs ( called enhancer RNAs) based on epigenomic classification [3]. Promoter-associated lncRNAs, like protein-coding mRNAs, are relatively stable, often spliced lncRNAs in Endothelial Cells Hypoxia and polyadenylated, whereas enhancer RNAs (eRNAs) tend to lack these modifications and are generally unstable [4]. LncRNA expression is exquisitely cell type-specific and is often perturbed in disease states [5, 6], suggesting functions in development, homeostasis and maintenance of cell identity

Methods

Results

Conclusion