High throughput CRISPRi screen identifies viability lncRNAs in human monocytes

Long noncoding RNAs are emerging as critical regulators of biological processes. While there are over 20,000 lncRNAs annotated in the human genome we do not know the function for the majority. Here we performed a high-throughput CRISPRi screen to identify those lncRNAs that are important in viability in human monocytes using the cell line THP1. We identified a total of 35 hits from the screen and validated and characterized two of the top intergenic hits. The first is a lncRNA neighboring the macrophage viability transcription factor IRF8 (RP11-542M13.2 hereafter referred to as long noncoding RNA regulator of monocyte proliferation, LNCRMP) and the second is a lncRNA celled OLMALINC (oligodendrocyte maturation-associated long intervening non-coding RNA) that was previously characterized to be important in oligodendrocyte maturation. Removal of LNCRMP and OLMALINC from monocytes severely limited their proliferation capabilities. RNA-seq analysis of knockdown lines showed that LNCRMP regulated proapoptotic pathways while knockdown of OLMALINC impacted genes associated with the cell cycle. This research highlights the importance of high-throughput screening as a powerful tool for quickly discovering functional long non-coding RNAs (lncRNAs) that play a vital role in regulating monocyte viability. Overall design: THP1 CRISPRi expressing cells were infected with lentivirual containing single guide RNAs (sgRNAs) targeting OLMALINC or LNCRMP. The infected cell were then selected with puromycin for 7 days. After 7 days of selection, total rna was collected and illumina based RNA sequencing was performed.