Cardiac endothelial cells maintain open chromatin and expression of cardiomyocyte myofibrillar genes.

Nora Yucel,Yifan Yang,Zoltan Arany,Jessie Axsom,Joshua H Rhoades,Li Li

doi:10.7554/elife.55730

Abstract

Endothelial cells (ECs) are widely heterogenous depending on tissue and vascular localization. Jambusaria et al. recently demonstrated that ECs in various tissues surprisingly possess mRNA signatures of their underlying parenchyma. The mechanism underlying this observation remains unexplained, and could include mRNA contamination during cell isolation, in vivo mRNA paracrine transfer from parenchymal cells to ECs, or cell-autonomous expression of these mRNAs in ECs. Here, we use a combination of bulk RNASeq, single-cell RNASeq datasets, in situ mRNA hybridization, and most importantly ATAC-Seq of FACS-isolated nuclei, to show that cardiac ECs actively express cardiomyocyte myofibril (CMF) genes and have open chromatin at CMF gene promoters. These open chromatin sites are enriched for sites targeted by cardiac transcription factors, and closed upon expansion of ECs in culture. Together, these data demonstrate unambiguously that the expression of CMF genes in ECs is cell-autonomous, and not simply a result of technical contamination or paracrine transfers of mRNAs, and indicate that local cues in the heart in vivo unexpectedly maintain fully open chromatin in ECs at genes previously thought limited to cardiomyocytes.

Highlights

Endothelial cells (ECs) are the most abundant non-blood cells in the body, and form the inner layer of all vessels in all organs
In addition to accessibility at promoter-transcriptional start sites (TSSs) regions, most peaks associated with enhancer regions of cardiomyocyte marker genes were seen in cardiac ECs (Figure 4—figure supplement 1A–B) We did identify a small number of enhancer regions that were unique to the non-EC nuclei, including an enhancer region upstream of the gene encoding the cardiac transcription factor Nkx25, and an intronic enhancer within the Dmd gene (Figure 4—figure supplement 1C)
We show here that cardiac ECs possess transcriptional and epigenetic signatures of cardiomyocytes, but not other cell types within the heart

Summary

Introduction

Endothelial cells (ECs) are the most abundant non-blood cells in the body, and form the inner layer of all vessels in all organs. ECs carry out a wide range of critical functions, including providing a barrier between blood and the underlying parenchyma, regulating transport of nutrients and waste across that barrier, regulation of immune cell extravasation, maintaining intravascular hemostatic homeostasis, and controlling blood flow and systemic vascular resistance These numerous roles differ widely depending on anatomical site, developmental stage, and physiological state. We show that cardiac ECs maintain chromatin accessibility and transcriptional activation of myofibrillar genes typical of underlying cardiomyocyte parenchyma, but not of the immediately surrounding stromal cells.

Results

Discussion

TSS Enrichment

Materials and methods