Flores-Arenas Cristina, Malekos Eric, Montano Christy, Covarrubias Sergio, Sudek Lisa, Dempsey Valory, Huynh Vuky, Katzman Sol, Carpenter Susan
Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, California, USA.
Department of Biomolecular Engineering, University of California Santa Cruz, California, USA.
J Biol Chem. 2025 May 7;301(6):110204. doi: 10.1016/j.jbc.2025.110204.
Long noncoding RNAs are emerging as critical regulators of biological processes. While there are over 36,000 lncRNAs annotated in the human genome, we do not know the function of the majority. Here, we performed a high-throughput CRISPRi screen to identify those lncRNAs that are important for viability in human monocytes using the cell line THP1. We identified a total of 38 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 called OLMALINC (oligodendrocyte maturation-associated long intervening non-coding RNA) that was previously found to be important in oligodendrocyte maturation. Transcriptional repression 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. Data support both LNCRMP and OLMALINC functioning in cis to regulate their neighboring proteins that are also essential for THP1 cell growth. 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.
长链非编码RNA正逐渐成为生物过程的关键调节因子。虽然人类基因组中注释的长链非编码RNA超过36,000种，但我们对其中大多数的功能并不了解。在此，我们进行了一项高通量CRISPRi筛选，以确定那些对人单核细胞系THP1的生存能力至关重要的长链非编码RNA。我们从筛选中总共鉴定出38个命中基因，并对其中两个最显著的基因间命中基因进行了验证和表征。第一个是与巨噬细胞生存能力转录因子IRF8相邻的长链非编码RNA（以下简称RP11-542M13.2，单核细胞增殖的长链非编码RNA调节因子，LNCRMP），第二个是一种名为OLMALINC（少突胶质细胞成熟相关长链居间非编码RNA）的长链非编码RNA，此前发现它在少突胶质细胞成熟中很重要。单核细胞中LNCRMP和OLMALINC的转录抑制严重限制了它们的增殖能力。对敲低细胞系的RNA测序分析表明，LNCRMP调节促凋亡途径，而敲低OLMALINC则影响与细胞周期相关的基因。数据支持LNCRMP和OLMALINC均以顺式作用调节其邻近蛋白，这些蛋白对THP1细胞生长也至关重要。这项研究强调了高通量筛选作为快速发现功能性长链非编码RNA（lncRNA）的强大工具的重要性，这些长链非编码RNA在调节单核细胞生存能力中起着至关重要的作用。
