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2017 ; 45
(9
): 5458-5469
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The lncRNA VELUCT strongly regulates viability of lung cancer cells despite its
extremely low abundance
#MMPMID28160600
Seiler J
; Breinig M
; Caudron-Herger M
; Polycarpou-Schwarz M
; Boutros M
; Diederichs S
Nucleic Acids Res
2017[May]; 45
(9
): 5458-5469
PMID28160600
show ga
Little is known about the function of most non-coding RNAs (ncRNAs). The majority
of long ncRNAs (lncRNAs) is expressed at very low levels and it is a matter of
intense debate whether these can be of functional relevance. Here, we identified
lncRNAs regulating the viability of lung cancer cells in a high-throughput RNA
interference screen. Based on our previous expression profiling, we designed an
siRNA library targeting 638 lncRNAs upregulated in human cancer. In a functional
siRNA screen analyzing the viability of lung cancer cells, the most prominent hit
was a novel lncRNA which we called Viability Enhancing LUng Cancer Transcript
(VELUCT). In silico analyses confirmed the non-coding properties of the
transcript. Surprisingly, VELUCT was below the detection limit in total RNA from
NCI-H460 cells by RT-qPCR as well as RNA-Seq, but was robustly detected in the
chromatin-associated RNA fraction. It is an extremely low abundant lncRNA with an
RNA copy number of less than one copy per cell. Blocking transcription with
actinomycin D revealed that VELUCT RNA was highly unstable which may partially
explain its low steady-state concentration. Despite its extremely low abundance,
loss-of-function of VELUCT with three independent experimental approaches in
three different lung cancer cell lines led to a significant reduction of cell
viability: Next to four individual siRNAs, also two complex siPOOLs as well as
two antisense oligonucleotides confirmed the strong and specific phenotype. In
summary, the extremely low abundant lncRNA VELUCT is essential for regulation of
cell viability in several lung cancer cell lines. Hence, VELUCT is the first
example for a lncRNA that is expressed at a very low level, but has a strong
loss-of-function phenotype. Thus, our study proves that at least individual
low-abundant lncRNAs can play an important functional role.
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