Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types

Cell Rep. 2022 Dec 27;41(13):111893. doi: 10.1016/j.celrep.2022.111893.

Abstract

Within the scope of the FANTOM6 consortium, we perform a large-scale knockdown of 200 long non-coding RNAs (lncRNAs) in human induced pluripotent stem cells (iPSCs) and systematically characterize their roles in self-renewal and pluripotency. We find 36 lncRNAs (18%) exhibiting cell growth inhibition. From the knockdown of 123 lncRNAs with transcriptome profiling, 36 lncRNAs (29.3%) show molecular phenotypes. Integrating the molecular phenotypes with chromatin-interaction assays further reveals cis- and trans-interacting partners as potential primary targets. Additionally, cell-type enrichment analysis identifies lncRNAs associated with pluripotency, while the knockdown of LINC02595, CATG00000090305.1, and RP11-148B6.2 modulates colony formation of iPSCs. We compare our results with previously published fibroblasts phenotyping data and find that 2.9% of the lncRNAs exhibit a consistent cell growth phenotype, whereas we observe 58.3% agreement in molecular phenotypes. This highlights that molecular phenotyping is more comprehensive in revealing affected pathways.

Keywords: CAGE; CP: Molecular biology; CP: Stem cell research; functional annotation; gapmer ASO; iPSC; long non-coding RNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Embryonic Stem Cells / metabolism
  • Gene Expression Profiling / methods
  • Humans
  • Induced Pluripotent Stem Cells* / metabolism
  • Oligonucleotides, Antisense
  • RNA, Long Noncoding* / genetics
  • RNA, Long Noncoding* / metabolism

Substances

  • RNA, Long Noncoding
  • Oligonucleotides, Antisense