The high-throughput perturbation of long non-coding RNA reveals functional features in stem cells and across cell-types

Yip, C. W.; Hon, C.-C.; Yasuzawa, K.; Mundackal Sivaraman, D.; Ramilowski, J. A.; Shibayama, Y.; Agrawal, S.; Prabhu, A. V.; Parr, C.; Severin, J.; Lan, Y. J.; Dostie, J.; Nishiyori-Sueki, H.; Tagami, M.; Ito, M.; Lopez-Redondo, F.; Kouno, T.; Chang, J.-C.; Luginbuhl, J.; Kato, M.; Murata, M.; Yip, W. H.; Shu, X.; Abugessaisa, I.; Hasegawa, A.; Suzuki, H.; Yagi, K.; Kasukawa, T.; de Hoon, M. J. L.; Carninci, P.; Shin, J. W.

doi:10.1101/2022.02.16.480297

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bioRxiv · 10.1101/2022.02.16.480297

The high-throughput perturbation of long non-coding RNA reveals functional features in stem cells and across cell-types

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Abstract

Within the scope of FANTOM6 consortium, we perform a large-scale knockdown of 200 long non-coding RNAs (lncRNAs) in human induced pluripotent stem (iPS) cells, 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 iPS cells. We compare our results with previously published fibroblasts phenotyping data and find that 2.9% of the lncRNAs exhibit consistent cell growth phenotype, whereas we observe 58.3% agreement in molecular phenotypes. This highlights molecular phenotyping is more comprehensive in revealing affected pathways.

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Yip, C. W., Hon, C.-C., Yasuzawa, K., Mundackal Sivaraman, D., Ramilowski, J. A., Shibayama, Y., Agrawal, S., Prabhu, A. V., Parr, C., Severin, J., Lan, Y. J., Dostie, J., Nishiyori-Sueki, H., Tagami, M., Ito, M., Lopez-Redondo, F., Kouno, T., Chang, J.-C., Luginbuhl, J., Kato, M., Murata, M., Yip, W. H., Shu, X., Abugessaisa, I., Hasegawa, A., Suzuki, H., Yagi, K., Kasukawa, T., de Hoon, M. J. L., Carninci, P., Shin, J. W.. 2022-02-18. The high-throughput perturbation of long non-coding RNA reveals functional features in stem cells and across cell-types. https://doi.org/10.1101/2022.02.16.480297

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