Human vault RNAs exhibit diverse expression patterns and inter-locus compensation

In 1986, a class of small, noncoding RNAs was discovered in association with an enormous, enigmatic ribonucleoprotein complex – the “vault” particle – and thus dubbed vault RNAs (vtRNAs). However, it’s since been recognized that the vast majority (≥95%) of these noncoding vtRNA molecules are not associated with the mysterious vaults, raising questions about their potential independent function(s). Moreover, humans express four vtRNAs from two different loci, and debate has arisen about whether the vtRNA paralogs share any functional connection, and whether they should remain classified together. Herein, we report the expression patterns of the four VTRNA paralogs in a variety of human cell lines, including various single- and multi-gene VTRNA -knockout cell lines. Knockout of one or more of the three VTRNA1 genes leads to increased expression of vtRNA2-1, suggesting that their biological functions are related. Additionally, we interrogated the effects of vtRNA knockout on HEK293T cell growth, viability, and viral infection, and were unable to replicate previously reported associations. Collectively, our findings point to a potential functional connection between even the most distantly related human vtRNA paralogs, while reaffirming that their biological roles and mechanisms still require critical study.