Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

Ramilowski, J. A.; Yip, C. W.; Agrawal, S.; Chang, J.-C.; Ciani, Y.; Kulakovskiy, I. V.; Mendez, M.; Ooi, J. L. C.; Petri, A.; Roos, L.; Severin, J.; Yasuzawa, K.; Ouyang, J. F.; Parkinson, N.; Abugessaisa, I.; Akalin, A.; Antonov, I.; Arner, E.; Bonetti, A.; Bono, H.; Borsari, B.; Brombacher, F.; Cannistraci, C.; Cardenas, R.; Cardon, M.; Chang, H.; Dostie, J.; Ducoli, L.; Favorov, A.; Fort, A.; Garrido, D.; Gil, N.; Gimenez, J.; Guler, R.; Handoko, L.; Harshbarger, J.; Hasegawa, A.; Hasegawa, Y.; Hashimoto, K.; Hayatsu, N.; Heutink, P.; Hirose, T.; Imada, E. L.; Itoh, M.; Kaczkowski, B.; Kan

doi:10.1101/700864

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bioRxiv · 10.1101/700864

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

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Abstract

Long non-coding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes and yet, their functions remain largely unknown. We systematically knockdown 285 lncRNAs expression in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNA exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest to-date lncRNA knockdown dataset with molecular phenotyping (over 1,000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.

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Ramilowski, J. A., Yip, C. W., Agrawal, S., Chang, J.-C., Ciani, Y., Kulakovskiy, I. V., Mendez, M., Ooi, J. L. C., Petri, A., Roos, L., Severin, J., Yasuzawa, K., Ouyang, J. F., Parkinson, N., Abugessaisa, I., Akalin, A., Antonov, I., Arner, E., Bonetti, A., Bono, H., Borsari, B., Brombacher, F., Cannistraci, C., Cardenas, R., Cardon, M., Chang, H., Dostie, J., Ducoli, L., Favorov, A., Fort, A., Garrido, D., Gil, N., Gimenez, J., Guler, R., Handoko, L., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, K., Hayatsu, N., Heutink, P., Hirose, T., Imada, E. L., Itoh, M., Kaczkowski, B., Kan. 2019-07-14. Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping. https://doi.org/10.1101/700864

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