Establishment of a body-wide non-coding RNA cell type enrichment atlas, with a focus on endothelial enriched non-coding gene function

In this proposal, we plan to generate a publicly accessible cell type specificity atlas for human non-protein coding RNAs (ncRNAs), and to investigate the function of those enriched in endothelial cells.

There are >20,000 known ncRNAs, a diverse group of genes that can have important regulatory functions, but little is known about their expression profiles, making determination of their role in cell biology challenging; the vast majority have no annotated function.

We will use an integrated correlation-based analysis of bulk RNA sequencing data, to profile ncRNA enrichment signatures in over 70 cell types from over 20 different human organs, a method we previously developed and validated for the profiling of protein coding genes.

The data we generate will be available on the Human Protein Atlas (HPA) portal, providing body-wide, cell-type enrichment signatures for all sequenced ncRNAs.

We will perform a cross-tissue analysis to identify ncRNAs with EC enrichment in multiple tissue beds and validate their expression profile using fluorescence in situ hybridization.

We will knockdown or overexpress these candidates in cultured primary ECs, and determine their role in various cell specific functions, such as response to inflammatory cytokines, growth factors, hypoxia, shear stress, interactions with blood leucocytes and regulation of coagulation.

This project will create an important tool for the study of ncRNA biology, as well providing insight into endothelial ncRNA biology.