Profiling of HeLa nucleoplasmic and nucleolar RNAs by Halo-seq proximity labeling

Ahola, T.; Takabe, P.; Salomaki, R.; Lillsunde, P.; Bahrudeen, M.; Wlodkowic, D.; Kaslin, J.; Efimov, A.; Anko, M.-L.

doi:10.64898/2026.01.29.702496

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bioRxiv · 10.64898/2026.01.29.702496

Profiling of HeLa nucleoplasmic and nucleolar RNAs by Halo-seq proximity labeling

Ahola, T.·Takabe, P.·Salomaki, R.·Lillsunde, P.·Bahrudeen, M.·Wlodkowic, D.·Kaslin, J.·Efimov, A.·Anko, M.-L.

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Abstract

Subcellular RNA localization is a key regulator of gene expression, but transcriptome wide characterization of RNAs enriched in specific cellular compartments has been hindered by methodological limitations in throughput and spatial resolution. Halo-seq is an RNA proximity-labeling approach that enables the extraction of RNAs located near virtually any Halo-tagged bait protein. However, its broader application has been restricted by the limited availability of the required Halo ligand. Here we present a Halo-seq dataset profiling the nucleoplasmic and nucleolar transcriptomes of HeLa cells. Through experimental and computational validation, we demonstrate that our optimized Halo-seq protocol achieves high spatial specificity, enabling robust mapping of compartment-enriched RNA populations.

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Ahola, T., Takabe, P., Salomaki, R., Lillsunde, P., Bahrudeen, M., Wlodkowic, D., Kaslin, J., Efimov, A., Anko, M.-L.. 2026-01-30. Profiling of HeLa nucleoplasmic and nucleolar RNAs by Halo-seq proximity labeling. https://doi.org/10.64898/2026.01.29.702496

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